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.)

Ultimate Spider-Man

First strike, haste
Camouflage — {2}: Put a +1/+1 counter on Ultimate Spider-Man. He gains hexproof and becomes colorless until end of turn.
Whenever you attack, double the number of each kind of counter on each Spider and legendary creature you control.

Miles Morales

When Miles Morales enters, put a +1/+1 counter on each of up to two target creatures.
{3}{R}{G}{W}: Transform Miles Morales. Activate only as a sorcery.

Miles Morales // Ultimate Spider-Man

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}.

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.)

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.

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.

Mist-Syndicate Naga

Ninjutsu {2}{U} ({2}{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, create a token that's a copy of this creature.

Spider-Ham, Peter Porker

When Spider-Ham enters, create a Food token. (It's an artifact with "{2}, {T}, Sacrifice this token: You gain 3 life.")
Animal May-Ham — Other Spiders, Boars, Bats, Bears, Birds, Cats, Dogs, Frogs, Jackals, Lizards, Mice, Otters, Rabbits, Raccoons, Rats, Squirrels, Turtles, and Wolves you control get +1/+1.

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.)

Satoru, the Infiltrator

Menace
Whenever Satoru and/or one or more other nontoken creatures you control enter, if none of them were cast or no mana was spent to cast them, draw a card.

Throat Slitter

Ninjutsu {2}{B} ({2}{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, destroy target nonblack creature that player controls.

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.

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.

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.)

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.

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.

SP//dr, Piloted by Peni

Vigilance
When SP//dr enters, put a +1/+1 counter on target creature.
Whenever a modified creature you control deals combat damage to a player, draw a card. (Equipment, Auras you control, and counters are modifications.)

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.

Blade-Blizzard Kitsune

Ninjutsu {3}{W} ({3}{W}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Double strike

Spiders-Man, Heroic Horde

Web-slinging {4}{G}{G} (You may cast this spell for {4}{G}{G} if you also return a tapped creature you control to its owner's hand.)
When Spiders-Man enters, if they were cast using web-slinging, you gain 3 life and create two 2/1 green Spider creature tokens with reach.

Amazing Spider-Man

Vigilance, reach
Each legendary spell you cast that's one or more colors has web-slinging {G}{W}{U}. (You may cast a spell for its web-slinging cost if you also return a tapped creature you control to its owner's hand.)

Peter Parker

When Peter Parker enters, create a 2/1 green Spider creature token with reach.
{1}{G}{W}{U}: Transform Peter Parker. Activate only as a sorcery.

Peter Parker // Amazing Spider-Man

Walker of Secret Ways

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, look at that player's hand.
{1}{U}: Return target Ninja you control to its owner's hand. Activate only during your turn.

Araña, Heart of the Spider

Whenever you attack, put a +1/+1 counter on target attacking creature.
Whenever a modified creature you control deals combat damage to a player, exile the top card of your library. You may play that card this turn. (Equipment, Auras you control, and counters are modifications.)

Spring-Leaf Avenger

Ninjutsu {3}{G} ({3}{G}, 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, return target permanent card from your graveyard to your hand.

Silk, Web Weaver

Web-slinging {1}{G}{W} (You may cast this spell for {1}{G}{W} if you also return a tapped creature you control to its owner's hand.)
Whenever you cast a creature spell, create a 1/1 green and white Human Citizen creature token.
{3}{G}{W}: Creatures you control get +2/+2 and gain vigilance until end of turn.

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.

Spider-Punk

Riot (This creature enters with your choice of a +1/+1 counter or haste.)
Other Spiders you control have riot.
Spells and abilities can't be countered.
Damage can't be prevented.

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.

Resourceful Defense

Whenever a permanent you control leaves the battlefield, if it had counters on it, put those counters on target permanent you control.
{4}{W}: Move any number of counters from target permanent you control onto a second target permanent you control.

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.)

Scarlet Spider, Ben Reilly

Web-slinging {R}{G} (You may cast this spell for {R}{G} if you also return a tapped creature you control to its owner's hand.)
Trample
Sensational Save — If Scarlet Spider was cast using web-slinging, he enters with X +1/+1 counters on him, where X is the mana value of the returned creature.

Thousand-Faced Shadow

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.)
Flying
When this creature enters from your hand, if it's attacking, create a token that's a copy of another target attacking creature. The token enters tapped and attacking.

Wastes

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.

Spider-Sense

Web-slinging {U} (You may cast this spell for {U} if you also return a tapped creature you control to its owner's hand.)
Counter target instant spell, sorcery spell, or triggered 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.)

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.

Spider-Man, Brooklyn Visionary

Web-slinging {2}{G} (You may cast this spell for {2}{G} if you also return a tapped creature you control to its owner's hand.)
When Spider-Man enters, search your library for a basic land card, put it onto the battlefield tapped, then shuffle.

Mistblade Shinobi

Ninjutsu {U} ({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 return target creature that player controls to its owner's hand.

Daily Bugle Building

{T}: Add {C}.
{1}, {T}: Add one mana of any color.
Smear Campaign — {1}, {T}: Target legendary creature gains menace until end of turn. Activate only as a sorcery.

Skullsnatcher

Ninjutsu {B} ({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, exile up to two target cards from that player's graveyard.

Spider-Man India

Web-slinging {1}{G}{W} (You may cast this spell for {1}{G}{W} if you also return a tapped creature you control to its owner's hand.)
Pavitr's Sevā — Whenever you cast a creature spell, put a +1/+1 counter on target creature you control. It gains flying until end of turn.

Azra Smokeshaper

Ninjutsu {1}{B} ({1}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
When this creature enters, target creature you control gains indestructible until end of turn.

Spider-UK

Web-slinging {2}{W} (You may cast this spell for {2}{W} if you also return a tapped creature you control to its owner's hand.)
At the beginning of your end step, if two or more creatures entered the battlefield under your control this turn, you draw a card and gain 2 life.

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.

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.")