Lim-Dûl's Vault

Look at the top five cards of your library. As many times as you choose, you may pay 1 life, put those cards on the bottom of your library in any order, then look at the top five cards of your library. Then shuffle and put the last cards you looked at this way on top in any order.

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 the battlefield as a copy of any creature on the battlefield, except it's a Ninja in addition to its other creature types.

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.

Rivendell

Rivendell enters the battlefield tapped unless you control a legendary creature.
{T}: Add {U}.
{1}{U}, {T}: Scry 2. Activate only if you control a legendary creature.

Silver Shroud Costume

Flash
When Silver Shroud Costume enters the battlefield, attach it to target creature you control. That creature gains shroud until end of turn. (It can't be the target of spells or abilities.)
Equipped creature can't be blocked.
Equip {3}

Temple of Deceit

Temple of Deceit enters the battlefield tapped.
When Temple of Deceit enters the battlefield, scry 1.
{T}: Add {U} or {B}.

Path of Ancestry

Path of Ancestry enters the battlefield tapped.
{T}: Add one mana of any color in your commander's color identity. When that mana is spent to cast a creature spell that shares a creature type with your commander, scry 1. (Look at the top card of your library. You may put that card on the bottom.)

Sol Ring

The Black Gate

As The Black Gate enters the battlefield, you may pay 3 life. If you don't, it enters the battlefield tapped.
{T}: Add {B}.
{1}{B}, {T}: Choose a player with the most life or tied for most life. Target creature can't be blocked by creatures that player controls this turn.

Rogue Class

(Gain the next level as a sorcery to add its ability.)
Whenever a creature you control deals combat damage to a player, exile the top card of that player's library face down. You may look at it for as long as it remains exiled.
{1}{U}{B}: Level 2
Creatures you control have menace.
{2}{U}{B}: Level 3
You may play cards exiled with Rogue Class, and you may spend mana as though it were mana of any color to cast those spells.

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.

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.)

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 the battlefield this turn.

Ingenious Prodigy

Skulk (This creature can't be blocked by creatures with greater power.)
Ingenious Prodigy enters the battlefield with X +1/+1 counters on it.
At the beginning of your upkeep, if Ingenious Prodigy has one or more +1/+1 counters on it, you may remove a +1/+1 counter from it. If you do, draw a card.

Diabolic Tutor

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

Dimir Signet

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.

Command Tower

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

Spectral Sailor

Flash (You may cast this spell any time you could cast an instant.)
Flying
{3}{U}: Draw a card.

Dimir Infiltrator

Dimir Infiltrator can't be blocked.
Transmute {1}{U}{B} ({1}{U}{B}, Discard this card: Search your library for a card with the same mana value as this card, reveal it, put it into your hand, then shuffle. Transmute only as a sorcery.)

Mist-Cloaked Herald

Quietus Spike

Equipped creature has deathtouch.
Whenever equipped creature deals combat damage to a player, that player loses half their life, rounded up.
Equip {3}

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 the battlefield, target creature you control gains deathtouch and lifelink until end of turn.

Wingcrafter

Soulbond (You may pair this creature with another unpaired creature when either enters the battlefield. They remain paired for as long as you control both of them.)
As long as Wingcrafter is paired with another creature, both creatures have flying.

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.

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.

Faerie Seer

Flying
When Faerie Seer enters the battlefield, scry 2.

Ornithopter

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 Throat Slitter deals combat damage to a player, destroy target nonblack creature that player controls.

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.

Kaito Shizuki

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

Okiba-Gang Shinobi

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 Okiba-Gang Shinobi deals combat damage to a player, that player discards two cards.

Swiftfoot Boots

Equipped creature has hexproof and haste. (It can't be the target of spells or abilities your opponents control.)
Equip {1}

Bojuka Bog

Bojuka Bog enters the battlefield tapped.
When Bojuka Bog enters the battlefield, exile target player's graveyard.
{T}: Add {B}.

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}.

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 the battlefield from your hand, if it's attacking, create a token that's a copy of another target attacking creature. The token enters the battlefield tapped and attacking.

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.

Sword Coast Sailor

Commander creatures you own have "Whenever this creature attacks a player, if no opponent has more life than that player, this creature can't be blocked this turn."

Whispersilk Cloak

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

Slither Blade

Brainstorm

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

Lightning Greaves

Equipped creature has haste and shroud. (It can't be the target of spells or abilities.)
Equip {0}

Thought Vessel

You have no maximum hand size.
{T}: Add {C}.

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.

Tormented Soul

Tormented Soul can't block and can't be blocked.

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.

Siren Stormtamer

Flying
{U}, Sacrifice Siren Stormtamer: Counter target spell or ability that targets you or a creature you control.

Tetsuko Umezawa, Fugitive

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

Preordain

Scry 2, then draw a card. (To 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.)

Bident of Thassa

Whenever a creature you control deals combat damage to a player, you may draw a card.
{1}{U}, {T}: Creatures your opponents control attack this turn if able.

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."

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.

Fellwar Stone

{T}: Add one mana of any color that a land an opponent controls could produce.

Feed the Swarm

Destroy target creature or enchantment an opponent controls. You lose life equal to that permanent's mana value.

Covert Technician

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 Covert Technician deals combat damage to a player, you may put an artifact card with mana value less than or equal to that damage from your hand onto the battlefield.

Serum Visions

Throatseeker

Unblocked attacking Ninjas you control have lifelink.

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 the battlefield, return up to one target creature to its owner's hand.

Lórien Revealed

Draw three cards.
Islandcycling {1} ({1}, Discard this card: Search your library for an Island card, reveal it, put it into your hand, then shuffle.)

Invisible Stalker

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

Gingerbrute

Haste
{1}: Gingerbrute can't be blocked this turn except by creatures with haste.
{2}, {T}, Sacrifice Gingerbrute: You gain 3 life.

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 Skullsnatcher deals combat damage to a player, exile up to two target cards from that player's graveyard.

Biting-Palm Ninja

Ninjutsu {2}{B}
Biting-Palm Ninja enters the battlefield 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.

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 of your library.)

Talisman of Dominance

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

Satoru, the Infiltrator

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

Reliquary Tower

Crystal Ball

{1}, {T}: Scry 2. (Look at the top two cards of your library, then put any number of them on the bottom of your library and the rest on top in any order.)

Baleful Strix

Flying, deathtouch
When Baleful Strix enters the battlefield, draw a 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.

Arcane Signet

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 the battlefield, target creature you control gains indestructible until end of turn.

Counterspell

Creeping Tar Pit

Creeping Tar Pit enters the battlefield tapped.
{T}: Add {U} or {B}.
{1}{U}{B}: Creeping Tar Pit becomes a 3/2 blue and black Elemental creature until end of turn and can't be blocked this turn. It's still a land.

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.

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.