Shadowmage Infiltrator

Fear (This creature can't be blocked except by artifact creatures and/or black creatures.)
Whenever Shadowmage Infiltrator deals combat damage to a player, you may draw a card.

Tetsuko Umezawa, Fugitive

Creatures you control with power or toughness 1 or less 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.")

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.

Counterspell

Talisman of Dominance

{T}: Add {C}.
{T}: Add {U} or {B}. Talisman of Dominance deals 1 damage to you.

Shirei, Shizo's Caretaker

Whenever a creature with power 1 or less is put into your graveyard from the battlefield, you may return that card to the battlefield at the beginning of the next end step if Shirei, Shizo's Caretaker is still on the battlefield.

Jon Irenicus, Shattered One

At the beginning of your end step, target opponent gains control of up to one target creature you control. Put two +1/+1 counters on it and tap it. It's goaded for the rest of the game and it gains "This creature can't be sacrificed." (It attacks each combat if able and attacks a player other than you if able.)
Whenever a creature you own but don't control attacks, you draw a card.

Inkfathom Infiltrator

Inkfathom Infiltrator can't block and can't be blocked.

Brainsurge

Draw four cards, then put two cards from your hand on top of your library in any order.

Candlekeep Sage

Commander creatures you own have "When this creature enters or leaves the battlefield, draw a card."

Vault of Whispers

The Myriad Pools

(Transforms from The Everflowing Well.)
{T}: Add {U}.
Whenever you cast a permanent spell using mana produced by The Myriad Pools, up to one other target permanent you control becomes a copy of that spell until end of turn.

The Everflowing Well

When The Everflowing Well enters, mill two cards, then draw two cards.
Descend 8 — At the beginning of your upkeep, if there are eight or more permanent cards in your graveyard, transform The Everflowing Well.

The Everflowing Well // The Myriad Pools

Rilsa Rael, Kingpin

Deathtouch
When Rilsa Rael, Kingpin enters, you take the initiative.
Whenever you attack, target attacking creature gains deathtouch until end of turn. If you've completed a dungeon, that creature also gets +5/+0 and gains first strike and menace until end of turn.

Homicide Investigator

Whenever one or more nontoken creatures you control die, investigate. This ability triggers only once each turn. (Create a Clue token. It's an artifact with "{2}, Sacrifice this artifact: Draw a card.")

Demonic Tutor

Search your library for a card, put that card into your hand, then shuffle.

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.

Sarevok, Deathbringer

At the beginning of each player's end step, if no permanents left the battlefield this turn, that player loses X life, where X is Sarevok's power.
Choose a Background (You can have a Background as a second commander.)

Mukotai Ambusher

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.)
Lifelink

Safana, Calimport Cutthroat

Menace
At the beginning of your end step, if you have the initiative, create a Treasure token. Create three of those tokens instead if you've completed a dungeon.
Choose a Background (You can have a Background as a second commander.)

Looter il-Kor

Shadow (This creature can block or be blocked by only creatures with shadow.)
Whenever Looter il-Kor deals damage to an opponent, draw a card, then discard a card.

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.

Sensei's Divining Top

{1}: Look at the top three cards of your library, then put them back in any order.
{T}: Draw a card, then put Sensei's Divining Top on top of its owner's library.

Swamp

Accursed Marauder

When Accursed Marauder enters, each player sacrifices a nontoken creature of their choice.

Sneaky Snacker

Flying
When you draw your third card in a turn, return Sneaky Snacker from your graveyard to the battlefield tapped.

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."

Island

Jet Medallion

Black spells you cast cost {1} less to cast.

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.

Inkrise Infiltrator

Flying
{3}{B}: Inkrise Infiltrator gets +2/+2 until end of turn.

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}.

Dokuchi Shadow-Walker

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.)

Strix Serenade

Counter target artifact, creature, or planeswalker spell. Its controller creates a 2/2 blue Bird creature token with flying.

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.

Their Name Is Death

Gitaxian Mindstinger

Deathtouch
Whenever Gitaxian Mindstinger deals combat damage to a player or battle, draw a card.

Aetherblade Agent

Deathtouch
{4}{U/P}: Transform Aetherblade Agent. Activate only as a sorcery. ({U/P} can be paid with either {U} or 2 life.)

Aetherblade Agent // Gitaxian Mindstinger

The Immortal Sun

Players can't activate planeswalkers' loyalty abilities.
At the beginning of your draw step, draw an additional card.
Spells you cast cost {1} less to cast.
Creatures you control get +1/+1.

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.