Forest

Mountain

Bebop, Skull & Crossbones

Partner with Rocksteady, Mutant Marauder (When this creature enters, target player may put Rocksteady into their hand from their library, then shuffle.)
Deathtouch
Whenever Bebop deals combat damage to a player, you may draw X cards, where X is the number of counters on Bebop. If you do, you lose X life.

Michelangelo, the Heart

Trample
Raid (the Fridge) — At the beginning of your second main phase, if you attacked this turn, put a +1/+1 counter on target creature and create a Food token.
Partner—Character select (You can have two commanders if both have this ability.)

Leonardo, the Balance

Whenever a token you control enters, you may put a +1/+1 counter on each creature you control. Do this only once each turn.
{W}{U}{B}{R}{G}: Creatures you control gain menace, trample, and lifelink until end of turn.
Partner—Character select (You can have two commanders if both have this ability.)

Raphael, the Muscle

Double all damage that creatures you control with counters on them would deal.
When Raphael enters, create a Mutagen token.
Partner—Character select (You can have two commanders if both have this ability.)

Dimension X Pizzasaur

When this creature enters, put two +1/+1 counters on target creature. When you do, destroy up to one target creature with mana value less than or equal to the number of counters among permanents you control.
{2}, {T}, Sacrifice this creature: You gain 3 life and each opponent loses 3 life.

Krang, the All-Powerful

If a player drawing a card causes a triggered ability of a permanent you control to trigger, that ability triggers an additional time.
Whenever a player draws their second card each turn, put a +1/+1 counter on Krang.

Swamp

Splinter, the Mentor

Menace
Whenever Splinter or another nontoken creature you control leaves the battlefield, create a Mutagen token.
Partner—Character select (You can have two commanders if both have this ability.)

April O'Neil, Live on the Scene

Whenever a Mutant, Ninja, or Turtle you control enters, investigate. (Create a Clue token. It's an artifact with "{2}, Sacrifice this token: Draw a card.")
Partner—Character select

Rat King, Pale Piper

Menace
Whenever Rat King or another nontoken creature you control leaves the battlefield, create a 1/1 black Rat creature token.
{2}, Sacrifice a token: Draw a card.

Donatello, the Brains

If one or more tokens would be created under your control, those tokens plus a Mutagen token are created instead.
Partner—Character select (You can have two commanders if both have this ability.)

Plains

Ray Fillet, Wave Warrior

Flying
Evolve (Whenever a creature you control enters, if that creature has greater power or toughness than this creature, put a +1/+1 counter on this creature.)
Whenever a creature you control with a counter on it deals combat damage to a player, draw a card.

Irma, Part-Time Mutant

At the beginning of combat on your turn, Irma becomes a copy of up to one other target creature you control, except her name is Irma, Part-Time Mutant and she has this ability. Then put a +1/+1 counter on her.

Shredder, Shadow Master

Whenever Shredder attacks a player, for each other opponent, create a token that's a copy of Shredder tapped and attacking that player, except it isn't legendary. Sacrifice those tokens at end of combat.
Whenever Shredder deals combat damage to a player, that player loses half their life, rounded up.

Casey Jones, Back Alley Brute

Menace
Whenever Casey Jones attacks, put a +1/+1 counter on target attacking creature.
Whenever you put one or more +1/+1 counters on a creature you control, Casey Jones deals that much damage to target opponent.

Baxter, Fly in the Ointment

Whenever Baxter enters or attacks, each creature you control with a counter on it gains flying until end of turn.
Whenever you draw a card, put a +1/+1 counter on Baxter.

Heroes in a Half Shell

Vigilance, menace, trample, haste
Whenever one or more Mutants, Ninjas, and/or Turtles you control deal combat damage to a player, put a +1/+1 counter on each of those creatures and draw a card.