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.)

Arcane Signet

{T}: Add one mana of any color in your commander's color identity.

Kaito, Cunning Infiltrator

Whenever a creature you control deals combat damage to a player, put a loyalty counter on Kaito.
+1: Up to one target creature you control can't be blocked this turn. Draw a card, then discard a card.
−2: Create a 2/1 blue Ninja creature token.
−9: You get an emblem with "Whenever a player casts a spell, you create a 2/1 blue Ninja creature token."

Forest

Command Tower

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.

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.

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.

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.)

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}.

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.

Swamp

Hot Dog Cart

When this artifact enters, create a Food token. (It's an artifact with "{2}, {T}, Sacrifice this token: You gain 3 life.")
{T}: Add one mana of any color.

Mountain

Plains

Tortoise Formation

Creatures you control gain shroud until end of turn. (They can't be the targets of spells or abilities.)

Taeko, the Patient Avalanche

Taeko enters tapped.
Whenever another creature you control leaves the battlefield, if it didn't die, scry 1 and put a +1/+1 counter on Taeko.
Whenever Taeko attacks, you may pay {U/B}. When you do, target attacking creature can't be blocked this turn.

Chromatic Lantern

Lands you control have "{T}: Add one mana of any color."
{T}: Add one mana of any color.

Ninja of the Deep Hours

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 this creature deals combat damage to a player, you may draw a card.

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.)

Counterspell

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.

Sakashima's Student

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.)
You may have this creature enter as a copy of any creature on the battlefield, except it's a Ninja in addition to its other creature types.

Donnie & April, Adorkable Duo

When Donnie & April enter, choose one or both. Each mode must target a different player.
• Target player draws two cards.
• Target player returns an artifact, instant, or sorcery card from their graveyard to their hand.

Ink-Eyes, Servant of Oni

Ninjutsu {3}{B}{B} ({3}{B}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever Ink-Eyes deals combat damage to a player, you may put target creature card from that player's graveyard onto the battlefield under your control.
{1}{B}: Regenerate Ink-Eyes.

Kaito Shizuki

At the beginning of your end step, if Kaito entered this turn, he phases out.
+1: Draw a card. Then discard a card unless you attacked this turn.
−2: Create a 1/1 blue Ninja creature token with "This token can't be blocked."
−7: You get an emblem with "Whenever a creature you control deals combat damage to a player, search your library for a blue or black creature card, put it onto the battlefield, then shuffle."

Commander's Sphere

{T}: Add one mana of any color in your commander's color identity.
Sacrifice this artifact: Draw a card.

Kappa Tech-Wrecker

Ninjutsu {1}{G}
This creature enters with a deathtouch counter on it.
Whenever this creature deals combat damage to a player, you may remove a deathtouch counter from it. When you do, exile target artifact or enchantment that player controls.

Reliquary Tower

You have no maximum hand size.
{T}: Add {C}.

Leonardo, Worldly Warrior

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

Subway Train

When this Vehicle enters, you may pay {G}. If you do, search your library for a basic land card, reveal it, put it into your hand, then shuffle.
Crew 2 (Tap any number of creatures you control with total power 2 or more: This Vehicle becomes an artifact creature until end of turn.)

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.)

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.

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.)

Sol Ring

Vibrant Cityscape

{T}, Sacrifice this land: Search your library for a basic land card, put it onto the battlefield tapped, then shuffle.

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.)

Island

Archelos, Lagoon Mystic

As long as Archelos is tapped, other permanents enter tapped.
As long as Archelos is untapped, other permanents enter untapped.

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.)

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.

Nashi, Moon Sage's Scion

Ninjutsu {3}{B} ({3}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever Nashi deals combat damage to a player, exile the top card of each player's library. Until end of turn, you may play one of those cards. If you cast a spell this way, pay life equal to its mana value rather than paying its mana cost.