Don & Leo, Problem Solvers

Vigilance
At the beginning of your end step, exile up to one target artifact you control and up to one target creature you control. Then return them to the battlefield under their owners' control.

Donatello, Mutant Mechanic

{T}: Put three +1/+1 counters on target artifact you control. If it isn't a creature, it becomes a 0/0 Robot creature in addition to its other types. Activate only as a sorcery.
Whenever an artifact you control is put into a graveyard from the battlefield, if it had counters on it, put those counters on up to one target artifact or creature you control.

Donatello, Gadget Master

Sneak {1}{U} (You may cast this spell for {1}{U} if you also return an unblocked attacker you control to hand during the declare blockers step. He enters tapped and attacking.)
Whenever Donatello deals combat damage to a player, create a token that's a copy of target artifact you control.

Turtles Forever

Search your library and/or outside the game for exactly four legendary creature cards you own with different names, then reveal those cards. An opponent chooses two of them. Put the chosen cards into your hand and shuffle the rest into your library.

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.)

Raphael, Tag Team Tough

Menace (This creature can't be blocked except by two or more creatures.)
Whenever Raphael deals combat damage to a player for the first time each turn, untap all attacking creatures. After this combat phase, there is an additional combat phase.

Raph & Mikey, Troublemakers

Trample, haste
Whenever Raph & Mikey attack, reveal cards from the top of your library until you reveal a creature card. Put that card onto the battlefield tapped and attacking and the rest on the bottom of your library in a random order.

Mikey & Don, Party Planners

Ward {2}
You may look at the top card of your library any time.
You may play lands and cast Mutant, Ninja, or Turtle spells from the top of your library. If you cast a creature spell this way, that creature enters with an additional +1/+1 counter on it.

Turtle Van

Whenever this Vehicle attacks, put a +1/+1 counter on target creature that crewed it this turn. Then if that creature is a Mutant, Ninja, or Turtle, double the number of +1/+1 counters on it.
Crew 1 (Tap any number of creatures you control with total power 1 or more: This Vehicle becomes an artifact creature until end of turn.)

Raph & Leo, Sibling Rivals

Whenever Raph & Leo attack, if it's the first combat phase of the turn, untap one or two target attacking creatures. After this phase, there is an additional combat phase.

Donatello, Rad Scientist

Vigilance (Attacking doesn't cause this creature to tap.)
When Donatello enters, tap up to three target creatures your opponents control. Put a stun counter on each of them. (If a permanent with a stun counter would become untapped, remove one from it instead.)

Leonardo, Worldly Warrior

Affinity for creatures (This spell costs {1} less to cast for each creature you control.)
Double strike (This creature deals both first-strike and regular combat damage.)

Swamp

Michelangelo's Technique

Sneak {3}{G} (You may cast this spell for {3}{G} if you also return an unblocked attacker you control to hand during the declare blockers step.)
Look at the top eight cards of your library. Put up to two creature cards with total mana value 6 or less from among them onto the battlefield and the rest on the bottom of your library in a random order.

Michelangelo, Improviser

Sneak {2}{G}{G} (You may cast this spell for {2}{G}{G} if you also return an unblocked attacker you control to hand during the declare blockers step. He enters tapped and attacking.)
Whenever Michelangelo deals combat damage to a player, you may put a creature card and/or a land card from your hand onto the battlefield.

Leonardo, Cutting Edge

Sneak {W} (You may cast this spell for {W} if you also return an unblocked attacker you control to hand during the declare blockers step. He enters tapped and attacking.)
Lifelink
Whenever you gain life, put a +1/+1 counter on Leonardo.

Slash, Reptile Rampager

Alliance — Whenever another creature you control enters, Slash deals 2 damage to each opponent.
Whenever Slash attacks, create a 2/2 red Mutant creature token.

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.)

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.

Leonardo, Sewer Samurai

Sneak {2}{W}{W}
Double strike
During your turn, you may cast creature spells with power or toughness 1 or less from your graveyard. If you cast a spell this way, that creature enters with a finality counter on it. (If a creature with a finality counter on it would die, exile it instead.)

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.)

Party Dude

(Gain the next level as a sorcery to add its ability.)
When this Class enters, each player creates a Food token.
{1}{G}: Level 2
Whenever an artifact an opponent controls is put into a graveyard from the battlefield, draw a card.
{4}{G}: Level 3
Whenever one or more of your opponents are attacked, up to one target attacking creature gets +X/+X until end of turn, where X is the number of cards in your hand.

Turtle Power!

Leader's Talent

(Gain the next level as a sorcery to add its ability.)
Whenever you attack, put a +1/+1 counter on target attacking creature.
{2}{W}: Level 2
Whenever a creature you control leaves the battlefield, if it had a counter on it, you gain 2 life.
{3}{W}: Level 3
Whenever you cast a spell, put a +1/+1 counter on each creature you control.

Mikey & Leo, Chaos & Order

Whenever you put a counter on a creature you control, draw a card. This ability triggers only once each turn.

Casey Jones, Vigilante

When Casey Jones enters, draw three cards. At the beginning of your next upkeep, discard three cards at random.

Raphael, Ninja Destroyer

Raphael must be blocked if able.
Enrage — Whenever Raphael is dealt damage, add that much {R}. Until end of turn, you don't lose this mana as steps and phases end.

Raphael, the Nightwatcher

Sneak {1}{R}{R} (You may cast this spell for {1}{R}{R} if you also return an unblocked attacker you control to hand during the declare blockers step. He enters tapped and attacking.)
Attacking creatures you control have double strike.

Splinter, Radical Rat

If an ability of a Ninja creature you control triggers, that ability triggers an additional time.
{1}{U}: Target Ninja can't be blocked this turn.

Raphael's Technique

Sneak {2}{R} (You may cast this spell for {2}{R} if you also return an unblocked attacker you control to hand during the declare blockers step.)
Each player may discard their hand and draw seven cards.

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.)

Splinter's Technique

Sneak {1}{B} (You may cast this spell for {1}{B} if you also return an unblocked attacker you control to hand during the declare blockers step.)
Search your library for a card, put that card into your hand, then shuffle.

Leonardo's Technique

Sneak {1}{W} (You may cast this spell for {1}{W} if you also return an unblocked attacker you control to hand during the declare blockers step.)
Return one or two target creature cards each with mana value 3 or less from your graveyard to the battlefield.

The Ooze

Whenever a creature you control with a +1/+1 counter on it leaves the battlefield, create a Mutagen token for each +1/+1 counter on it. (A Mutagen token is an artifact with "{1}, {T}, Sacrifice this token: Put a +1/+1 counter on target creature. Activate only as a sorcery.")
{T}: Exile target card from a graveyard. Create a Mutagen token.

Michelangelo, Weirdness to 11

When Michelangelo enters, create a Mutagen token. (It's an artifact with "{1}, {T}, Sacrifice this token: Put a +1/+1 counter on target creature. Activate only as a sorcery.")
If one or more +1/+1 counters would be put on a creature you control, that many plus one +1/+1 counters are put on it instead.

Don & Raph, Hard Science

Menace
Whenever Don & Raph attack, the next noncreature spell you cast this turn has affinity for artifacts. (It costs {1} less to cast for each artifact you control.)

Michelangelo, On the Scene

Trample (This creature can deal excess combat damage to the player it's attacking.)
Michelangelo enters with a +1/+1 counter on him for each land you control.
When Michelangelo dies, return this card to your hand.