Wolverine, Best There Is

Unrivaled Lethality — Double all damage Wolverine would deal.
At the beginning of each end step, if Wolverine dealt damage to another creature this turn, put a +1/+1 counter on him.
{1}{G}: Regenerate Wolverine. (The next time he would be destroyed this turn, instead tap him, remove him from combat, and heal all damage on him.)

Three Visits

Search your library for a Forest card, put it onto the battlefield, then shuffle.

Jenova, Ancient Calamity

At the beginning of combat on your turn, put a number of +1/+1 counters equal to Jenova's power on up to one other target creature. That creature becomes a Mutant in addition to its other types.
Whenever a Mutant you control dies during your turn, you draw cards equal to its power.

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.

Farseek

Search your library for a Plains, Island, Swamp, or Mountain card, put it onto the battlefield tapped, then shuffle.

Birds of Paradise

Indoraptor, the Perfect Hybrid

Bloodthirst X (This creature enters with X +1/+1 counters on it, where X is the damage dealt to your opponents this turn.)
Menace
Enrage — Whenever Indoraptor is dealt damage, choose an opponent at random. Indoraptor deals damage equal to its power to that player unless they sacrifice a nontoken creature of their choice.

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.

Evolution Witness

{1}{G}: Adapt 2. (If this creature has no +1/+1 counters on it, put two +1/+1 counters on it.)
Whenever one or more +1/+1 counters are put on this creature, return target permanent card from your graveyard to your hand.

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.

Yuriko, the Tiger's Shadow

Commander ninjutsu {U}{B} ({U}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand or the command zone tapped and attacking.)
Whenever a Ninja you control deals combat damage to a player, reveal the top card of your library and put that card into your hand. Each opponent loses life equal to that card's mana value.

Agent Frank Horrigan

Trample
Agent Frank Horrigan has indestructible as long as it attacked this turn.
Whenever Agent Frank Horrigan enters or attacks, proliferate twice. (To proliferate, choose any number of permanents and/or players, then give each another counter of each kind already there.)

Delighted Halfling

{T}: Add {C}.
{T}: Add one mana of any color. Spend this mana only to cast a legendary spell, and that spell can't be countered.

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.)

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.

Changeling Outcast

Changeling (This card is every creature type.)
This creature can't block and can't be blocked.

Nature's Lore

Search your library for a Forest card, put that card onto the battlefield, then shuffle.

Silver-Fur Master

Ninjutsu {U}{B} ({U}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Ninjutsu abilities you activate cost {1} less to activate.
Other Ninja and Rogue creatures you control get +1/+1.

Satoru Umezawa

Whenever you activate a ninjutsu ability, look at the top three cards of your library. Put one of them into your hand and the rest on the bottom of your library in any order. This ability triggers only once each turn.
Each creature card in your hand has ninjutsu {2}{U}{B}.

Roaming Throne

Ward {2}
As this creature enters, choose a creature type.
This creature is the chosen type in addition to its other types.
If a triggered ability of another creature you control of the chosen type triggers, it triggers an additional time.

Jason Bright, Glowing Prophet

Whenever a Zombie or Mutant you control dies, if its power was different from its base power, draw a card.
Come Fly With Me — {2}, Sacrifice a creature: Put a +1/+1 counter on target creature you control. It gains flying until end of turn.

Ingenious Infiltrator

Ninjutsu {U}{B} ({U}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever a Ninja you control deals combat damage to a player, draw a card.

Fallen Shinobi

Ninjutsu {2}{U}{B} ({2}{U}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever this creature deals combat damage to a player, that player exiles the top two cards of their library. Until end of turn, you may play those cards without paying their mana costs.

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.)

Hancock, Ghoulish Mayor

Each other creature you control that's a Zombie or Mutant gets +X/+X, where X is the number of counters on Hancock.
Undying (When this creature dies, if it had no +1/+1 counters on it, return it to the battlefield under its owner's control with a +1/+1 counter on it.)

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'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.

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.)

Kaito, Bane of Nightmares

Ninjutsu {1}{U}{B} ({1}{U}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
During your turn, as long as Kaito has one or more loyalty counters on him, he's a 3/4 Ninja creature and has hexproof.
+1: You get an emblem with "Ninjas you control get +1/+1."
0: Surveil 2. Then draw a card for each opponent who lost life this turn.
−2: Tap target creature. Put two stun counters on it.

Yuffie, Materia Hunter

Ninjutsu {1}{R} ({1}{R}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
When Yuffie enters, gain control of target noncreature artifact for as long as you control Yuffie. Then you may attach an Equipment you control to Yuffie.

Bloom Tender

Vivid — {T}: For each color among permanents you control, add one mana of that color.

Higure, the Still Wind

Ninjutsu {2}{U}{U} ({2}{U}{U}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever Higure deals combat damage to a player, you may search your library for a Ninja card, reveal it, put it into your hand, then shuffle.
{2}: Target Ninja creature can't be blocked this turn.

Faeburrow Elder

Vigilance
This creature gets +1/+1 for each color among permanents you control.
{T}: For each color among permanents you control, add one mana of that color.

Prosperous Thief

Ninjutsu {1}{U} ({1}{U}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever one or more Ninja or Rogue creatures you control deal combat damage to a player, create a Treasure token. (It's an artifact with "{T}, Sacrifice this token: Add one mana of any color.")