Base Roster:

Leonardo
Raphael
Michelangelo
Donatello
Leatherhead
April O'Neil
Wingnut
Karai
Bebop
Shredder (Oroku Saki)
Neo-Shredder (Oroku Hiroto)
Irma
Chrome Dome

Season One:
Ronin (TMNT: Last Ronin)
Jennika (TMNT IDW)
Krang
Rocksteady
Throttle (Biker Mice from Mars)

Season Two:

Splinter
Baxter
Alopex
Casey Jones
Mona Lisa
Rash (Battletoads)

Season Three:

Slash
Tiger Claw
Hun
Rahzar
Metalhead
Miyamoto Usagi (Usagi Yojimbo)