Loyal Apprentice

Haste
Lieutenant — At the beginning of combat on your turn, if you control your commander, create a 1/1 colorless Thopter artifact creature token with flying. That token gains haste until end of turn.

Kaito, Dancing Shadow

Whenever one or more creatures you control deal combat damage to a player, you may return one of them to its owner's hand. If you do, you may activate loyalty abilities of Kaito twice this turn rather than only once.
+1: Up to one target creature can't attack or block until your next turn.
0: Draw a card.
−2: Create a 2/2 colorless Drone artifact creature token with deathtouch and "When this creature leaves the battlefield, each opponent loses 2 life and you gain 2 life."

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, Moon Sage's Scion 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.

Baleful Strix

Flying, deathtouch
When Baleful Strix enters, 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, the Still Wind 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.

Professional Face-Breaker

Menace
Whenever one or more creatures you control deal combat damage to a player, create a Treasure token.
Sacrifice a Treasure: Exile the top card of your library. You may play that card this turn.

Phoenix Chick

Flying, haste
Phoenix Chick can't block.
Whenever you attack with three or more creatures, you may pay {R}{R}. If you do, return Phoenix Chick from your graveyard to the battlefield tapped and attacking with a +1/+1 counter on it.

Slither Blade

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.

Xander's Lounge

({T}: Add {U}, {B}, or {R}.)
Xander's Lounge enters tapped.
Cycling {3} ({3}, Discard this card: Draw a card.)

Moonsnare Specialist

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.)
When Moonsnare Specialist enters, return up to one target creature to its owner's hand.

Faerie Seer

Flying
When Faerie Seer enters, scry 2. (Look at the top two cards of your library, then put any number of them on the bottom and the rest on top in any order.)

Silent-Blade Oni

Ninjutsu {4}{U}{B} ({4}{U}{B}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever Silent-Blade Oni deals combat damage to a player, look at that player's hand. You may cast a spell from among those cards without paying its mana cost.

Gingerbrute

Haste (This creature can attack and {T} as soon as it comes under your control.)
{1}: Gingerbrute can't be blocked this turn except by creatures with haste.
{2}, {T}, Sacrifice Gingerbrute: You gain 3 life.

Steam Vents

({T}: Add {U} or {R}.)
As Steam Vents enters, you may pay 2 life. If you don't, it enters tapped.

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 Fallen Shinobi 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.

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.

Command Tower

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

Tin Street Dodger

Haste
{R}: Tin Street Dodger can't be blocked this turn except by creatures with defender.

Goro-Goro and Satoru

Whenever one or more creatures you control that entered this turn deal combat damage to a player, create a 5/5 red Dragon Spirit creature token with flying.
{1}{R}: Creatures you control gain haste until end of turn.

Dokuchi Silencer

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.)
Whenever Dokuchi Silencer deals combat damage to a player, you may discard a creature card. When you do, destroy target creature or planeswalker that player controls.

Gudul Lurker

Gudul Lurker can't be blocked.
Megamorph {U} (You may cast this card face down as a 2/2 creature for {3}. Turn it face up any time for its megamorph cost and put a +1/+1 counter on it.)

Watery Grave

({T}: Add {U} or {B}.)
As Watery Grave enters, you may pay 2 life. If you don't, it enters tapped.

Grim Hireling

Whenever one or more creatures you control deal combat damage to a player, create two Treasure tokens.
{B}, Sacrifice X Treasures: Target creature gets -X/-X until end of turn. Activate only as a sorcery.

Moon-Circuit Hacker

Ninjutsu {U} ({U}, Return an unblocked attacker you control to hand: Put this card onto the battlefield from your hand tapped and attacking.)
Whenever Moon-Circuit Hacker deals combat damage to a player, you may draw a card. If you do, discard a card unless Moon-Circuit Hacker entered this turn.

Triton Shorestalker

Changeling Outcast

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

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 artifact: Add one mana of any color.")

Nezumi Prowler

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 Nezumi Prowler enters, target creature you control gains deathtouch and lifelink until end of turn.

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 Walker of Secret Ways 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.

Invisible Stalker

Hexproof (This creature can't be the target of spells or abilities your opponents control.)
Invisible Stalker can't be blocked.

Nether Traitor

Haste
Shadow (This creature can block or be blocked by only creatures with shadow.)
Whenever another creature is put into your graveyard from the battlefield, you may pay {B}. If you do, return Nether Traitor from your graveyard to the battlefield.

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 Ninja of the Deep Hours deals combat damage to a player, you may draw a card.

Sunken Hollow

({T}: Add {U} or {B}.)
Sunken Hollow enters tapped unless you control two or more basic lands.

Thalakos Seer

Shadow (This creature can block or be blocked by only creatures with shadow.)
When Thalakos Seer leaves the battlefield, draw a card.

Reconnaissance Mission

Whenever a creature you control deals combat damage to a player, you may draw a card.
Cycling {2} ({2}, Discard this card: Draw a card.)

Crumbling Necropolis

Crumbling Necropolis enters tapped.
{T}: Add {U}, {B}, or {R}.

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 Thousand-Faced Shadow 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.

Moonblade Shinobi

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 Moonblade Shinobi deals combat damage to a player, create a 1/1 blue Illusion creature token with flying.

Warstorm Surge

Whenever a creature you control enters, it deals damage equal to its power to any target.

Kaito Shizuki

At the beginning of your end step, if Kaito Shizuki 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 creature 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."

Grazilaxx, Illithid Scholar

Whenever a creature you control becomes blocked, you may return it to its owner's hand.
Whenever one or more creatures you control deal combat damage to a player, draw a card.

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 Azra Smokeshaper enters, target creature you control gains indestructible until end of turn.

Dragon Tempest

Whenever a creature you control with flying enters, it gains haste until end of turn.
Whenever a Dragon you control enters, it deals X damage to any target, where X is the number of Dragons you control.

Mist-Cloaked Herald

Alora, Merry Thief

Whenever you attack, up to one target attacking creature can't be blocked this turn. Return that creature to its owner's hand at the beginning of the next end step.
Choose a Background (You can have a Background as a second commander.)

Biting-Palm Ninja

Ninjutsu {2}{B}
Biting-Palm Ninja enters with a menace counter on it.
Whenever Biting-Palm Ninja deals combat damage to a player, you may remove a menace counter from it. When you do, that player reveals their hand and you choose a nonland card from it. Exile that card.

Tetsuko Umezawa, Fugitive

Creatures you control with power or toughness 1 or less can't be blocked.

Cephalid Facetaker

Cephalid Facetaker can't be blocked.
At the beginning of combat on your turn, you may have Cephalid Facetaker become a copy of another target creature until end of turn, except it's 1/4 and has "This creature can't be blocked."

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, Servant of Oni 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.

Dragon's Hoard

Whenever a Dragon you control enters, put a gold counter on Dragon's Hoard.
{T}, Remove a gold counter from Dragon's Hoard: Draw a card.
{T}: Add one mana of any color.

Blood Crypt

({T}: Add {B} or {R}.)
As Blood Crypt enters, you may pay 2 life. If you don't, it enters tapped.

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 Mist-Syndicate Naga deals combat damage to a player, create a token that's a copy of Mist-Syndicate Naga.

Hammer of Purphoros

Creatures you control have haste.
{2}{R}, {T}, Sacrifice a land: Create a 3/3 colorless Golem enchantment artifact creature token.

Urabrask the Hidden

Creatures you control have haste.
Creatures your opponents control enter tapped.

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.

Cunning Evasion

Whenever a creature you control becomes blocked, you may return it to its owner's hand.