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.

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.

Aqueous Form

Enchant creature
Enchanted creature can't be blocked.
Whenever enchanted creature attacks, scry 1. (Look at the top card of your library. You may put that card on the bottom.)

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}.

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.")

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.

Whispersilk Cloak

Equipped creature can't be blocked and has shroud. (It can't be the target of spells or abilities.)
Equip {2}

Orochi Soul-Reaver

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 one or more creatures you control deal combat damage to a player, create a Treasure token and manifest the top card of that player's library. (Put it onto the battlefield face down as a 2/2 creature. Turn it face up any time for its mana cost if it's a creature card.)

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 Mistblade Shinobi deals combat damage to a player, you may return target creature that player controls to its owner's hand.

Palinchron

Flying
When Palinchron enters, untap up to seven lands.
{2}{U}{U}: Return Palinchron to its owner's hand.

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.

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.

Training Grounds

Activated abilities of creatures you control cost {2} less to activate. This effect can't reduce the mana in that cost to less than one mana.

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.

Cloak of Invisibility

Enchant creature
Enchanted creature has phasing and can't be blocked except by Walls. (It phases in or out before its controller untaps during each of their untap steps. While it's phased out, it's treated as though it doesn't exist.)

Blighted Agent

Infect (This creature deals damage to creatures in the form of -1/-1 counters and to players in the form of poison counters.)
Blighted Agent can't be blocked.

Bone Dancer

Whenever Bone Dancer attacks and isn't blocked, you may put the top creature card of defending player's graveyard onto the battlefield under your control. If you do, Bone Dancer assigns no combat damage this turn.

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.

Bouncing Beebles

Bouncing Beebles can't be blocked as long as defending player controls an artifact.

Aether Tunnel

Enchant creature
Enchanted creature gets +1/+0 and can't be blocked.

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.

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.

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.

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.)

Artful Dodge

Target creature can't be blocked this turn.
Flashback {U} (You may cast this card from your graveyard for its flashback cost. Then exile it.)

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.

Locus of Enlightenment

Locus of Enlightenment has each activated ability of the exiled cards used to craft it. You may activate each of those abilities only once each turn.
Whenever you activate an ability that isn't a mana ability, copy it. You may choose new targets for the copy.

The Enigma Jewel

The Enigma Jewel enters tapped.
{T}: Add {C}{C}. Spend this mana only to activate abilities.
Craft with four or more nonlands with activated abilities {8}{U} ({8}{U}, Exile this artifact, Exile the four or more from among other permanents you control and/or cards in your graveyard: Return this card transformed under its owner's control. Craft only as a sorcery.)

The Enigma Jewel // Locus of Enlightenment

Benthic Infiltrator

Devoid (This card has no color.)
Ingest (Whenever this creature deals combat damage to a player, that player exiles the top card of their library.)
Benthic Infiltrator can't be blocked.

Heartstone

Activated abilities of creatures cost {1} less to activate. This effect can't reduce the mana in that cost to less than one mana.

Clockwork Droid

You may exert Clockwork Droid as it attacks. When you do, it can't be blocked this turn and you scry 1. (An exerted creature won't untap during your next untap step. To scry 1, look at the top card of your library. You may put that card on the bottom.)

Rogue's Passage

{T}: Add {C}.
{4}, {T}: Target 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 Sakashima's Student enter as a copy of any creature on the battlefield, except it's a Ninja in addition to its other creature types.

Changeling Outcast

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

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.

Awesome Presence

Enchant creature
Enchanted creature can't be blocked unless defending player pays {3} for each creature they control that's blocking it.