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.)

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."

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.")

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.

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.

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.

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.

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.

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.

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.)

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.

Throatseeker

Unblocked attacking Ninjas you control have lifelink.

Plains

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.

Swamp

Smoke Shroud

Enchant creature
Enchanted creature gets +1/+1 and has flying.
When a Ninja you control enters, you may return this card from your graveyard to the battlefield attached to that creature.

Island

Mountain

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.

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."

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.)

Phantom Ninja

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.)