That's far too vague, we don't even know what part of Mewtwo are you replacing. Is it a model replacement? Moveset or animation replacement?
If it's a model replacement, generally it'll go over PlMtNr.dat, or over PlMt.dat if it's a moveset replacement. In the unlikely event it's only an animation replacement, it'd go over PlMtAJ.dat.
Quick explanation of what file does what (where XX is .dat character name, like Mt for Mewtwo, ZZ is color name):
-PlXX.dat = moveset edit
-PlXXZZ.dat = model and texture file for specific costumes (some common ones are Nr = Neutral, Gr = Green, Bu = Blue, Re = Red)
NOTE: You can't just put a model + texture file over another costume. If it's meant for Nr and you put it in Bu, it'll crash.
-PlXXAJ.dat = animation data. It's possible to swap pre-existing animations on the same character with only PlXX.dat edit, so this one isn't usually replaced.
-PlXXDViWaitAJ.dat = no idea. Not ever replaced or used, and I haven't seen any explanation as to what it's contents do, but I'm pretty sure it doesn't contain animation data, it's far too small for that.
Next time, please be as specific as you possibly can if you want immediate and accurate help.