Dealing with a flying player with a super high CMD

So... I have this encounter I want to do.

I have a super agile 16th level halfling scout who is the intel officer for a thieves guild the party is trying to take down. He will be prepping an area in town with several 3 story buildings, throwing stuff down at them, shooting from cover, and being a highly mobile menace. He knows the party inside and out so I can use meta knowledge to plan counters to my party but one of them is quite the munchkin.

She used polymorph and clone to turn herself int a young red dragon and has a lot of ioun stones that have boosted her CMD all the way up to 71, mostly through her new 48 strength and equally high dex.

I need to have a counter for her flight, but I'm a bit stymied. I have tons of 3e books and 3rd party books but most of what I have can't account for something this ridiculously high.

I prefer to use mundane items, traps and the like. I can even have this scout bring in a monster or a caster to help.

But I need something guaranteed to ground this character.

I was thinking some gnomish net launchers with something that could shut her wings down, contact poison or some enhancement I can't think of, or maybe a spell combined with it.

I saw elsewhere here someone posted 3e's rules on tripping fliers, but I wanna hear second opinions from other people.

Nets are good for entangling, which will lower speed and give Dex penalties (which can cause falling on a Fly check failure, especially if they can't move the required distance for their maneuverability. The issue is that a net is generally only useful against a creature within one size category of you. As a halfling is Small and a Young Adult Red Dragon is Large, it usually won't work. I tend to rule that it's the net's size that matters, not the thrower, so if the halfling has a Medium-sized net it could, but they'd have a –2 penalty to attack for the size difference. It's still a touch attack, but there may also be non-proficiency penalties too.

A tanglefoot bag is a touch attack, and it will also entangle, but it will require a flying creature to make a DC 15 Reflex save or fall. Three or Four stories is only about 3d6 damage, but it's likely the best choice.

Otherwise, if there was a wizard minion with a familiar, the share spells ability would let them cast antimagic field on the familiar (possibly from a scroll if not powerful enough themselves). If it were a bat or a bird, it would just fly next to the dragon and if not suppress the dragon form, make all the ioun stones fall off to the ground, maybe break. I wouldn't require reattunement, but still have to pick them up and place them. If the familiar has enough movement, just fly down alongside the falling character until the hit the ground to make sure they don't turn back into a dragon or cast feather fall.

A wither limb spell on a wing will stop flying, but not sure how your scout would do that.

Nets are good for entangling, which will lower speed and give Dex penalties (which can cause falling on a Fly check failure, especially if they can't move the required distance for their maneuverability. The issue is that a net is generally only useful against a creature within one size category of you. As a halfling is Small and a Young Adult Red Dragon is Large, it usually won't work. I tend to rule that it's the net's size that matters, not the thrower, so if the halfling has a Medium-sized net it could, but they'd have a –2 penalty to attack for the size difference. It's still a touch attack, but there may also be non-proficiency penalties too.

A tanglefoot bag is a touch attack, and it will also entangle, but it will require a flying creature to make a DC 15 Reflex save or fall. Three or Four stories is only about 3d6 damage, but it's likely the best choice.

Otherwise, if there was a wizard minion with a familiar, the share spells ability would let them cast antimagic field on the familiar (possibly from a scroll if not powerful enough themselves). If it were a bat or a bird, it would just fly next to the dragon and if not suppress the dragon form, make all the ioun stones fall off to the ground, maybe break. I wouldn't require reattunement, but still have to pick them up and place them. If the familiar has enough movement, just fly down alongside the falling character until the hit the ground to make sure they don't turn back into a dragon or cast feather fall.

A wither limb spell on a wing will stop flying, but not sure how your scout would do that.

I WAS thinking of him hiring a beholder to sit in the window of a building and shut down her ridiculous amount of Ioun stones.

I also gave him dampen presence, deodorizing powder, Aura Alteration, and Boots of Soft Step to cut through all this player's means of finding him if he needs to go to ground.

As for the nets? oh no I was thinking these would be rated for huge creatures, bound up into gnomish-built net launchers. Either fired from windows or the rooves by minions ready to take the flier down if she tries to do any circle strafing with her breath weapon.

As for the idea with the familiar its entirely feasible. and if the caster can distract her with yeeting her stones he could use the same trick with the familiar to deliver the spell to her wing.

the beholder would also prevent her oracle cohort from using magic to heal the wing.

All the while my scout's dropping literal artillery grade explosives, poisoned shot, maybe even collapsing a wall or two onto them.

I like this. if you have any more ideas please share.

I also had an idea for the other characters of a Warpsword (Book of vile darkness) being left out where it can be found and cursed to cause rage at Will save DC 15 or attack the nearest living thing.

If your dealing with level 15+ then a spell caster can be a great way to deal with the party without even facing them head on.

the feat spell perfection (must be at least level 15 to get) allow the caster to pick one spell to add a metamagic feat to without increasing it's level or casting time (as well as doubling any numeric bonus for spell casting from other feats) a combination of seeking spell metamagic with a long ranged spell can let the caster cast a quickened (level ignored from perfection) long range seeker spell and a normal seeker long range spell in one round (just remember the limit of 9 spell level before adjustment, see the feat) from inside the building they are protecting and hitting his target just by knowing who he targets (no cover or concealment applied) and heaving a lookout tell him they are in (long) range.
the party would have to deal with a caster slinging spells at them from a fortified area without even knowing the exact location of the troublesome enemy. I had one levitating from a building withing the walls (he had cast stone wall and made slits for the spells to leave by) . He kept changing his elevation giving the party trouble pinpointing where he was.

I made a 'Phantom Zone' enforcer build on the spell perfection idea (might be over the cr, a level 20 sorcerer with the harrow bloodline). who had 2 spell perfections, one for ill omen spell (from his bloodline bonus spells) and one for plane shift (to add reach spell and hit from afar) who would hit his targets from medium range with a quickened ill omen and then send them via medium ranged plane shift (reach spell, as a level 7 spell it can't gain more then 2 level upgrades of metamagic so can't get long range on it) to his harrow bloodline ability pocket dimension where time doesn't move as long as he is not there (AKA the phantom zone). spell perfection also doubled his greater\spell focus(conjuration) and greater\spell penetration to help it hit harder. his other bloodline abilities -level 20 never flatfooted and active on Suprise rounds and his bloodline added spell of moment of prescience complemented his fighting abilities well. (it's a build meant to deal with enemies that can't\ shouldn't be killed. clone using or immortal foes etc, anything that can't step out of time-traps)

I like the idea of a beholder (never mind that it is very out of character for most beholders to work for lesser beings). Pair that with a bunch of Rogues waiting nearby (given that the enemy knows when and where the PCs are coming and can plan for this): AM cone to remove all the abilities from the 'dragon', watch it fall and take damage and end up prone, Rogues to run out and Sneak Attack the prone caster who is now hopefully very reduced in AC.

btw, it sounded like the clone-dragon used polymorph and then cloned the dragon to make herself a permanent dragon body. which should not work by the rules. the polymorphed caster is not a dragon, it never changed it's type and the growing period of the clone should have been well after the polymorphed flesh would return to normal and thus wouldn't grow into a dragon clone.

Also if she used specifically the Polymorph spell it never had an option to turn into a dragon. it allow: animals (also magical beasts), elementals and hominoids. but not dragons, for that she need form of the dragon or other high level spells like shapechange or polymorph any object. (still won't work with clone, but polymorph any object used right can have a permanent duration).

before looking for ways to deal with the character in game, you might want to look into how she got to be OP from the start. it smells.

Another way to deal wth flying characters (doesnt work always but can work) is mundane or magical wind.
It imposes a penalty to all fly checks and a lot of flying movements (especially in a small area with lots of obstacles) need a fly check to succeed.
A lot of people i know only try to get the +14 on fly (check her size and maneuverability for potential boni/mali) to auto succeed the DC 15 check to hover. A penalty (or combination of penalties, like tanglefooot back, net, sickend, shaken etc) can make it really difficult to fly with her wings in a way she wants to.

There is also a DC 25 check if you collide with a object of your size or smaller to not hit the ground. A few traps with boulders, walls etc with her siza (medium or large i guess) could bring her down easily if she hasnt invested enough into her fly skill.

Its normally not that hard to impose the shaken condition and a tanglefoot bag to a creature if I know it. That would be a -4 penatly (-2 shaken and -4 Dex because she is entagled, so another -2)

I agree with zza ni on this... something doesn't smell right.

That being said, try Gravity Well. Doesn't need to be a spell-caster, it can be a large rune in the center of an area that has some bait she can't resist, and once activated, covers a 'large' range/area. Anti-Magic Shell is another good one.

The thing is, you're the GM, and it's a story. You don't need a way/reason, you just state what happens, and let them work around it. Ethereal Chains rise from the ground and wrap around her neck, pulling her downward. The rogue made a deal with a powerful entity or something... and as long as you're doing it for story-telling, and not gm-vs-player, she won't complain... She may ask "How?", and a spellcraft or arcane roll could tell her that aberrant power or something else thematic, is at work here. She doesn't need to know the specifics, unless of course, it comes across as a gm-vs-player thing.

Mechanics are super important, no doubt... players work HARD to get certain mechanics, and they don't 'need' to be countered, even if the enemy knows they exist... But story is even more important, and no player complains that their awesome mechanics are temporarily stymied, if there's a story at play. Just as long as it's obviously not a recurring thing, where what they thought makes them awesome, is constantly taken away.

My super stealthy Kineticist moves 960' per turn can 'Snipe' better than most anyone, and is all over the field (albeit, not with a 71 CMD nor 40-something stats :P). So I get where she's coming from, but I've many times lost my movement via reasons that have no game-mechanic I'm aware of... but my GM makes sure that, if he takes away something that makes a player special, he doesn't do it in a way that proves fatal. Stop her and she dies... there's gonna be trust issues, IMHO.

You should remember that the PC will not get the dragon BAB, feats, and skills even if he has a legitimate way to become a dragon.

Polymorph is very different between Pathfinder and 3.5.

Then there is the problem of stacking Ioun stones. For almost all of them duplicates are the "same source", and so don't stack.

Stacking: Stacking refers to the act of adding together bonuses or penalties that apply to one particular check or statistic. Generally speaking, most bonuses of the same type do not stack. Instead, only the highest bonus applies. Most penalties do stack, meaning that their values are added together. Penalties and bonuses generally stack with one another, meaning that the penalties might negate or exceed part or all of the bonuses, and vice versa.

To echo what others have said, you should really acquaint the player in question with the transmutation rules. Spells of the polymorph subschool "make you appear to be the creature," but "do not grant you all of the abilities and powers of the creature. Each polymorph spell allows you to assume the form of a creature of a specific type, granting you a number of bonuses to your ability scores and a bonus to your natural armor."

So you have to look at each individual spell to see what bonuses you get. In polymorph's case, you can only use it to turn into an animal (using the beast shape II spell rules), humanoid (using the alter self's spell rules), or elemental (using the elemental body I spell rules).

So, if the character in question cast polymorph to turn into an animal, he could not take any animal form. He could only take the form of a tiny, small, medium, or large animal (as per beast shape II). He would not automatically get all of that animal's abilities; he would only get that animal's abilities that were listed in the spell description. Likewise, he would not simply get that animal's ability scores; he would get the ability score bonuses and penalties listed in the spell description. For example, if that character took the form of a lion (a large animal), he would get a +4 size bonus to Strength, a –2 penalty to Dexterity, and a +4 natural armor bonus.

The same considerations would extend to a form of the dragon spell (which said character would need to take on the shape of a dragon). He would not get the statistics of a dragon. He would get what form of the dragon I (or II, or III) granted him. Nothing more, nothing less.

She used polymorph and clone to turn herself int a young red dragon

So, I'm guessing she used clone and then polymorph on the clone to make it the inert body of a young red dragon. That's a possible interpretation of how those may interact, but she should have run something like that by you first. I'd have probably just had that interrupt the cloning process entirely, causing the clone spell to fail.

But also there is this to keep that tactic from working:

The clone is physically identical to the original and possesses the same personality and memories as the original.

So, even if you'd transformed the clone before taking control of it, the magic of the clone spell would have reverted your form to being "physically identical to the original".

I don't see how.

Clone could certainly create a clone of a young red dragon. No issue there. Various magical shenanigans could then be used by the character to inhabit the cloned dragon form. That would give said character true draconic stats, but this also kind of renders the original scenario moot... because conventional combat tools are only going to go so far against characters with 8th level spells.

Regardless, spells of the polymorph subschool are limited to what they provide. If I'm missing something (either super obvious or subtle), please let me know--I'm happy to be wrong (and thus, learning) on stuff like this.

there are several ways this just does not add up. I assume the player knows the magic rules slightly better than the GM but I can't see how a dragon polymorph with CMB is much of a threat, more a paper dragon.

I'd also question the need to martially trump a caster with a rogue... you should try a caster or change the situation. Employing rent-a-beholder or using antimagic is just desperation. stop. You are going about it the wrong way.

So... I have this encounter I want to do.

I have a super agile 16th level halfling scout who is the intel officer for a thieves guild the party is trying to take down. He will be prepping an area in town with several 3 story buildings, throwing stuff down at them, shooting from cover, and being a highly mobile menace. He knows the party inside and out so I can use meta knowledge to plan counters to my party but one of them is quite the munchkin.

She used polymorph and clone to turn herself int a young red dragon and has a lot of ioun stones that have boosted her CMD all the way up to 71, mostly through her new 48 strength and equally high dex.

I need to have a counter for her flight, but I'm a bit stymied. I have tons of 3e books and 3rd party books but most of what I have can't account for something this ridiculously high.

I prefer to use mundane items, traps and the like. I can even have this scout bring in a monster or a caster to help.

But I need something guaranteed to ground this character.

I was thinking some gnomish net launchers with something that could shut her wings down, contact poison or some enhancement I can't think of, or maybe a spell combined with it.

I saw elsewhere here someone posted 3e's rules on tripping fliers, but I wanna hear second opinions from other people.

Are you actually playing D&D3.x or PF1? Or some combination of the two? Polymorphing works very differently in the two games (Form of the Dragon II would be the guideline for what adjustments a 'Large chromatic or metallic dragon' form would grant in PF1).

Even under 3.0/3.5 rules, a Young Red Dragon only had Str 25 and Dex 10*, so getting both of these stats up to 48ish definitely seems more than a little off.

*The PF1 version also has a Strength of 25 but a Dexterity of 12.

Rouges get UMD as a class skill, and Halflings shave a racial bonus to CHA. Give the rogue a staff of illusions. This gives him access to Mislead, Mirror Image and Major Image and a few other spells. Mislead gives you the greater invisibility and creates a duplicate that can distract the dragon. A few Major Images can create even more confusion. When the character chases down the rogue make sure mirror image is up so, that there is a good chance the attacks are wasted. Scrolls are fairly cheap so; give the rogue some scrolls with other spells to give him more options.

Just because a rogue is not a caster does not mean he cannot use magic.

I like this. if you have any more ideas please share.

Also, the Thieves' Guild has sponsored a local parade or food drive for the poor in that part of town, (or a 'Down With Red Dragon Infiltrators' protest) so there's lots of innocents. the other PCs need to be mindful of.

And someone's sent a message to a Very Old Gold or Silver Dragon nearby about a red dragon attacking their town. As soon as the red dragon starts flying, it comes out of the clouds and shrieks in draconic (hope the learned that language) that it won't tolerate this encroachment and full round claw/claw/bite them.

It won't listen to obvious lies about being a good guy. All the townspeople are terrified and screaming down below. Even if it doesn't kill the red dragon, it should distract them while they sort things out, but obviously if they keep attacking a small halfling (or apparently the buildings of town someone happens to be standing on), it should go all out.

alright... on GMming -
focusing on a PC as 'a problem'(which could be true) and competing with your player means things have gone awry. Remember, it's a Game and entertainment. You are there to tell a story, maybe teach some lessons, be fair and mostly follow the rules (a GM has more leeway), and have a good olde thyme. You're the director of a Play and owner of the stage, not one of the actors.

Rules -
AFAIK there's no way for a 15 Lvl PC to effectively pull off what you describe. Clone:N8 simply produces a duplicate (dead) body with the same ability scores & memories as the caster but only one can live. Usually Polymorph Any Obj is used at this point but you still need an animating soul and *that* falls into GM territory. Simulacrum is about the same route but produces an active half-power duplicate, again the GM has some say as to what the simulacrum has.
Polymorphing into a dragon just makes the caster bigger (no creature type change) and affects MIBS, sometimes casting, does NOT improve HPs, BAB, or attacks (as mfg weapons are better) but usually gives more attacks(natural attacks). It is a mixed bag. Fey Form & Undead Anatomy are better as it's about the immunities and movement while keeping casting.
IF you had said Magic Jar it would make more sense, but posessing a dragon will have consequences as they're not cuddly kittens and they tend to hold grudges. It's also a gift for the GM as the player has just provided an NPC motivation. A GMs job is all about consequences... so be a good GM, put on your cheshire cat smile and say "do your crazy stuff & show me what you got! Do IT!...I'll take notes".

A simple (Grtr) Bestow Curse, Baleful Polymorph, or Geas would shut all of this polymorphing down. I also like Magic Jarring the caster's old body as without it he's eventually a goner...
Think Trap the Soul gem with an inscribed name being worn by the dragon, once posessed by the named creature... well you can guess.

Build design -
look at the Mage-killer Build. It trades 2 levels of Wiz for martial abilities, saves, and close CM maneuvers. It's better than toying with levels of assassin or ninja.
If your desperate; 4 gunslingers, a buffing or dirge bard, and a diviner (focused on evocations) or illusionist (providing cover & distractions). That will pretty much put down anything at range.

Plot -
What's the story? characters? plot? drama? challenges? How does power & control shift back and forth? Motivations? What (if any) moral dilemma?(OMG- classic tragedies and ST:TOS) What lessons are there to learn? How do the challenges affect the psyche of the PCs?
So you have a rogue you want to use. Who else is in the guild? Who is calling the shots? Did someone pay to have this done or is it happenstance? colliding egos? jilted lovers/ex's/amores?
When at a loss, just pick up a random Cliff's Notes of a Shakespeare play and modify as needed. Clytemnestra is fun. Perhaps you want more drama?

Even under 3.0/3.5 rules, a Young Red Dragon only had Str 25 and Dex 10*, so getting both of these stats up to 48ish definitely seems more than a little off.

As Ion stones were cited, I have a strong suspicion that the PC brought several Pale Blue Rhomboid Ioun stoned and used them to enhance the dragon's strength, saying that they stack (they don't).

We are assuming a lot of bad things about the player, but what he did fails the smelly test.

For a really overpowered PC, the scout has positioned a covered mirror of opposition. A minion unveils it if the dragon flies up. Then, instead of actually attacking the PC (it can), it flies off around town and starts doing all sorts of [alignment-based] things. Now people hate the dragon PC.

Maybe the mirror also catches the minion, so there's a good minion fighting the original. And maybe, when the scout got the mirror, he actually cloned a good scout, that ran or was driven off (was outnumbered or something when it happened). Now he shows up a short time into the fight to help, but will the players just attack him on sight? Will they believe him that he's saying "I'm here to help!" or is it a trick?"

The dragon could try smashing the mirror to end the duplicate (if they know what it is, don't let them look it up), so the scout should have a plan to get it away or to safety, and the good scout won't want that to happen until the original scout is defeated or destroyed.

btw, it sounded like the clone-dragon used polymorph and then cloned the dragon to make herself a permanent dragon body. which should not work by the rules. the polymorphed caster is not a dragon, it never changed it's type and the growing period of the clone should have been well after the polymorphed flesh would return to normal and thus wouldn't grow into a dragon clone.

Also if she used specifically the Polymorph spell it never had an option to turn into a dragon. it allow: animals (also magical beasts), elementals and hominoids. but not dragons, for that she need form of the dragon or other high level spells like shapechange or polymorph any object. (still won't work with clone, but polymorph any object used right can have a permanent duration).

before looking for ways to deal with the character in game, you might want to look into how she got to be OP from the start. it smells.

NGL I argued this with her, but she argued she was dragon when the flesh was taken. However she's one of those players that reads all the alternative rules (especially the construct rules) and argued it was possible until I gave in. But I can't take it away from her at this point since its been a year IRL and kinda hard baked into the story at this point. We've also had a talk about her doing s~!* like this, and she has stopped, but its hard to deal with a character like this:

And she did this... in a city campaign that was supposed to be about intrigue and investigations.

To complicate things for her: I made it so Dragons can smell that she's a bastard dragon. they can smell her methods on her. I also gave her an NPC she has to watch because she's a kelpto with no survival instinct and if she dies a portal to hell opens. throw a noble title on her and she has to deal with the city's nobility.

I have also have got her hooked on conquering Castle Pescheour. From the apocalypse stone AD&D module, and all the problems that come with conquering it, and worse.

...

NGL I argued this with her, but she argued she was dragon when the flesh was taken. However she's one of those players that reads all the alternative rules (especially the construct rules) and argued it was possible until I gave in. But I can't take it away from her at this point since its been a year IRL and kinda hard baked into the story at this point. We've also had a talk about her doing s%#& like this, and she has stopped, but its hard to deal with a character like this:
It does bother me however that she saw fit to add 25 HD to her character and add it to her caster level, and throw the dragon's stats onto her own.
Str 48
Dex 34
Con 26
Int 34
Wis 30
Cha 28
How she got these stats? She added the dragon's stats to her own. a young dragon, but still a dragon. She also gets a big buff from her wayfinder of the stars giving her a massive buff to everything (and we're talking like 28 ioun stones in the Wayfinder)
-...

• Directly adding base stats and HD is not something you are allowed to do (seriously, this should never have got past the initial sniff test as it absolutely reeks of trouble),
• The Wayfinder of the Stars (which only holds ONE Ioun Stone as per the standard Wayfinder since any exceptions (like the Ebon Wayfinder) are specifically stated as such) shouldn't add any real power: It just points toward the nearest portal or teleports you to another planet, and
• The Stargazer prestige class doesn't seem to add any real power here either (beyond the AC bonus from the 'coat of many stars' at least).

Seems like there are a _lot_ of problems with her character, but aside from telling the player she did it wrong and depowering her to some reasonable level, I don't see much of a solution there in-game.

An in-game threat might be gunslingers. Add Distance to their guns, and they're targeting touch AC at a much longer range. The 7th-level Deed 'Targeting' lets them go for headshots, which cause Confusion for a round with no saving throw (assuming she's not also immune to mind-affecting effects through her seemingly infinite wealth). That will possibly turn her obscene stats against her allies for a while if you have a couple of gunslingers keeping her locked down.

Targeting also lets you target wings, but a DC 20 Fly check against a character of that level with a Dex of 34 is nothing. Maybe if you stack it with some high winds and other debuffs, but they're starting with a +12 just from Dex even if they don't have any ranks in it. Grounding them is probably more about environment than anything. Make them go into some areas with low ceilings and narrow corridors and they're not going to be flying (assuming they only fly because of their wings).

Time to introduce a Cyclopean Seer enemy and abuse its Flash of Insight ability (just joking)

How she got these stats? She added the dragon's stats to her own. a young dragon, but still a dragon. She also gets a big buff from her wayfinder of the stars giving her a massive buff to everything (and we're talking like 28 ioun stones in the Wayfinder)
- She's primarily a crafter with levels in stargazer and arcanist[Occultist]
- she also has a small platoon of custom made sheild guardian dolls with the advanced template, and can shoot 4 shots from double crossbows that do fire/bleed damage.
- And her familiar is a HD 17 celestial red panda with 14 levels of oracle that can somehow do 9th level spells.

Not to pile on, but when we're talking about someone that somehow got 28 ioun stones and when the trouble is they have a platoon of custom shield guardians, not just guardians, and how you say she has a familiar that can 'somehow cast 9th-level spells', there's a point where you have to take the responsibility.

That said, she's in the game, has been in the game, and right now you've asked how to make a good encounter that accounts for her, not whether she should be there or not. Hopefully some of the advice will help make this encounter memorable and not a stomping.

If you need something else to fix it... consider dropping a whole bunch of (possibly advanced) chaos beasts on top of her and hope one lands a corporeal instability. The DC to resume shape is only DC 15 (regardless of the DC to save or resist the curse), and you can always say that somehow she only resumes her 'true' shape (dragon is not her true shape, maybe if she was reincarnated). Even when the curse is fully removed, she's back in her true body (because CHAOS!), and yeah, it may not be spelled out in how the game works, but neither is any of the other stuff going on. And you let her play as a god for a year.

Copy her character sheet and have her fight herself.

Or just make a character that breaks all the rules like she did. If a player wants to powergame, I'll powergame, too. If a player has been allowed to break the rules then you need to break the rules too.

The REAL solution is to sit down with the player and explain that you made a mistake and in order to keep it fun and challenging (and less of a headache/ chore for you), the two of you need to sit down and unravel all the cheats to make the character "legal". I'm assuming you're friends. Friends can be forgiving when mistakes are made.

NGL I argued this with her, but she argued she was dragon when the flesh was taken. However she's one of those players that reads all the alternative rules (especially the construct rules) and argued it was possible until I gave in. But I can't take it away from her at this point since its been a year IRL and kinda hard baked into the story at this point. We've also had a talk about her doing s*$* like this, and she has stopped, but its hard to deal with a character like this:
It does bother me however that she saw fit to add 25 HD to her character and add it to her caster level, and throw the dragon's stats onto her own.
Str 48
Dex 34
Con 26
Int 34
Wis 30
Cha 28
How she got these stats? She added the dragon's stats to her own. a young dragon, but still a dragon. She also gets a big buff from her wayfinder of the stars giving her a massive buff to everything (and we're talking like 28 ioun stones in the Wayfinder)
-...

Its your game, so as a GM you can let her be or change it.

And if a player reads a LOT of rules and makes such a grave mistake I would question it if it wasnt intentional.
There is NOTHING in any rules that I know of that even suggest that you can to what she did.
Even if i read "clon" totally wrong (on purpose or on accident) I would only get that stats of a young red dragon, with an INT of 12 thats not that impressive and only 11 HD really sucks for all my spells.

She just plain cheated. If you dont address it, its ok. As said its your game, but she cheated.
I would address it, I wouldn't call her out for cheating (normally cheater dont respond well if they are caught and I´m a peacefull person who avoids trouble if necassery).
However I would tell her, like I said above, that I got a better unterstading of the rules thanks to the forum and that what she did was sadly not RAW and not even RAI, so she cant do that and that we have to build her charakter new and stripping some of its power.

Stats are hardly ever baked into a story, only flavour is.
She can be looking like a dragon and having the BAB of a wizard and her normal stats. Changes nothing in the story just makes her weaker (and by weaker I mean in this case, it makes her normal and not overpowered strong).
Let her look like a young red dragon and even keep her fly speed (with her being large and a poor fly speed so -6 to fly, so she has to invest a lot of skill points to keep flying if you bring up wind or some other ideas mentioned above OR just cast overland flight and fly with the spell and not her wings)

If you want the encounter to be memorable and NOT discuss this problem of her totally misunterstanding the rules, just copy her.
Let the rouge be whatever you like (he found a scroll clone and a scroll polymorph, so the same spells she used) and just add some monster stats to his own (and the monster abilites).
You can make him really fast with a quickling and he would be small. So a lot of walls with only small openings and a town where the streets are too small for a large dragon to fly would be his way to stay out of her way.
Let his to fighter companions also be some young red dragons (in armor, cause they are fighter) who alos used this trick.

The problem is:
her charakter is MUCH stronger than she should be.
You have a level 16 Rouge (thats like a CR 16 Monster, give or take) and want him to be a challange for a better version of a anciant red dragon (CR 19).
And the anciant red dragon has "only"
STR 38 (she has 48, so -10)
DEX 8 (she has 34, so -26)
CON 27 (she has 26, so + 1)
INT 20 (she has 34, so -14)
WIS 21 (she has 30, so - 9)
CHA 20 (she has 28, so - 8)

That more like a CR 20 or even CR 21 creature.
You are asking how a non-magical CR 16 creature can fight a magical CR 21 creature.
Well the answear is, he cant.
Even with all the tricks, the difference is to huge.
Thats why cheating is called cheating and why nobody expect the cheater likes it.

You can only make it interesting if you handle her as a CR 21 creature, and give the rouge a boost. So make him CR/level 21 or 22 (22 cause she has minions [her party but for her thats just minions at this point]) Like 6 times the advanced template. So +24 to all his abiliy scores and +12 natural armor.
Or make him a rouge 20 and only +2 advanced template (+8 to all abiliy scores and +4 natural armor)
Or any other template (or combination of templates) that pushes him +6 on his CR.
Or let there be 8 or them (8 CR 16 creatures are one CR 22 creature, and with the way pathfiner works, 8 small creatures are not as much a thread as 1 big creaure in most cases)
Or make him a ghost.

I hope you see HOW much he has to gain (and how stupid that would be) so that the encoutner would be interesting/challanging.
Only with mundane items and a few environmental tricks (wind/buildings/suprise round etc.) you can never hope to achieve a +6 difference in CR.
+1 yes, maybe +2, everything else is not really possible in PF.

So you have like 3 choices:
1) Talk to her and make her charakter right.
2) Let her be and up your game (like 6 advanced templates etc)
3) Let her stomp the encounter and encourage her cheating.

Just curious, how do the other players react to her? Do they moan and roll their eyes when she obliterates an encounter? Do they just sit back while she handles everything? Do they race to do as much damage before she ends the fight?
Does she intentionally take over the encounters? Des she give others a chance to shine?

I'm with Chuck Mount... a lot of this REALLY depends on the rest of the group.
If they're not even close to this one player in power the one player should fix their character and build it as per the rules because I can very nearly guarantee the rest of the players don't like playing with her.

Otherwise, build a custom mythic enemy that can use timestop on everyone else and make a custom magic spell or cursed item (because you've allowed her to create custom things she doesn't have a leg to stand on if she tries to say it's not fair that you did it) that reduces her to a regular character instead of this giant ball of misunderstanding (or cheating) cheese that she's created* that way it was done "in the story"

*(and, sadly, that you've allowed her to create and continue to play for the past year?!? Seriously, have you spoken with the group? Are they all having fun? If you haven't yet, talk to them all separately to hopefully get honest answers out of each of them.)

Actually, yeah, if you want to counter her, look through the mythic rules and create something with a decent amount of mythic ranks. You said you can use meta-knowledge so the mythic creature would know this one character is the largest threat and would therefore go for her first.

If there isn't something in the base Mythic rules to help enough, Legendary Games created a bunch of mythic content as well; check that out.

Pathfinder doesn't have clear rules to add character levels to a creature with racial HD and get a player character (what the player has done, even if starting from a character race). The existing rules are for NPC, where what matters is the creature CR, not the level.

That notwithstanding, she is now an 11 HD dragon with what, 20 levels in character classes? That is a CL of 31.
To increase her level by one using the rules for Beyond 20th Level in the CRB she would need 2,150,400,000 xp. "Only" seven million CR 20 monsters.
Her class advancement should have stopped as soon as she had completed her trick, as no single world can feed her the xp she needs to advance.

Oh, I forgot she had added 25 HD too. That would make her a 56th-level character. 72 million of billion of XP to increase her level.

All that riding on a Polymorph spell that somehow has become permanent.

Guess what?
It is still a Polymorph spell and it can still be canceled with a Dispel Magic spell, without save or spell resistance.
Mage's Disjunction would remove the need for a caster level check against the level of the Polymorph.

Guess what?
It is still a Polymorph spell and it can still be canceled with a Dispel Magic spell, without save or spell resistance.
Mage's Disjunction would remove the need for a caster level check against the level of the Polymorph.

Thats genius.

If she wants to do this trick again, just tell her that you have recently read how clone really works and that sadly, but for the better she cant copy it.

If would also have the benefit, that the party dont have any buffs on them at the start of the fight and that a few magic items dont work too.
So its a really good start for your rouge.