Read the Bones

Scry 2, then draw two cards. You lose 2 life. (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.)

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."

Feed the Swarm

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

Obelisk of Urd

Convoke (Your creatures can help cast this spell. Each creature you tap while casting this spell pays for {1} or one mana of that creature's color.)
As Obelisk of Urd enters, choose a creature type.
Creatures you control of the chosen type get +2/+2.

Telling Time

Look at the top three cards of your library. Put one of those cards into your hand, one on top of your library, and one on the bottom of your library.

Prowler's Helm

Equipped creature can't be blocked except by Walls.
Equip {2}

Rogue's Passage

{T}: Add {C}.
{4}, {T}: Target creature can't be blocked 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.

Death Denied

Return X target creature cards from your graveyard to your hand.

Ghoulcaller's Chant

Choose one —
• Return target creature card from your graveyard to your hand.
• Return two target Zombie cards from your graveyard to your hand.

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."

Satoru, the Infiltrator

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

Displacement Wave

Return all nonland permanents with mana value X or less to their owners' hands.

Command Tower

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

Sky Diamond

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.

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}.

Thassa, God of the Sea

Indestructible
As long as your devotion to blue is less than five, Thassa isn't a creature. (Each {U} in the mana costs of permanents you control counts toward your devotion to blue.)
At the beginning of your upkeep, scry 1.
{1}{U}: Target creature you control can't be blocked this turn.

Cancel

Island

Marang River Prowler

Marang River Prowler can't block and can't be blocked.
You may cast Marang River Prowler from your graveyard as long as you control a black or green permanent.

Dimir Aqueduct

Dimir Aqueduct enters tapped.
When Dimir Aqueduct enters, return a land you control to its owner's hand.
{T}: Add {U}{B}.

Tetsuko Umezawa, Fugitive

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

Dimir Keyrune

{T}: Add {U} or {B}.
{U}{B}: Dimir Keyrune becomes a 2/2 blue and black Horror artifact creature until end of turn and can't be blocked this turn.

Temple of Deceit

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

Vashta Nerada

Indestructible
Shadow (This creature can block or be blocked by only creatures with shadow.)
Morbid — At the beginning of each end step, if a creature died this turn, put a +1/+1 counter on Vashta Nerada.

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.

Changeling Outcast

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

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.

Submerged Boneyard

Submerged Boneyard enters tapped.
{T}: Add {U} or {B}.

Thriving Moor

Thriving Moor enters tapped. As it enters, choose a color other than black.
{T}: Add {B} or one mana of the chosen color.

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.

Slither Blade

Ghost of Ramirez DePietro

Ghost of Ramirez DePietro can't be blocked by creatures with toughness 3 or greater.
Whenever Ghost of Ramirez DePietro deals combat damage to a player, choose up to one target card in a graveyard that was discarded or put there from a library this turn. Put that card into its owner's hand.
Partner (You can have two commanders if both have partner.)

Counterspell

Brainstorm

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

Another Chance

You may mill two cards. Then return up to two creature cards from your graveyard to your hand. (To mill two cards, put the top two cards of your library into your graveyard.)

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.

Feywild Visitor

Commander creatures you own have "Whenever one or more nontoken creatures you control deal combat damage to a player, you create a 1/1 blue Faerie Dragon creature token with flying."

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.

Reliquary Tower

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

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.

Dispel

Didn't Say Please

Counter target spell. Its controller mills three cards.

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.

Invisible Stalker

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

Archetype of Imagination

Creatures you control have flying.
Creatures your opponents control lose flying and can't have or gain 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.")

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.

Lightning Greaves

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

Throatseeker

Unblocked attacking Ninjas you control have lifelink.

Sol Ring

Dark Petition

Search your library for a card, put that card into your hand, then shuffle.
Spell mastery — If there are two or more instant and/or sorcery cards in your graveyard, add {B}{B}{B}.

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.

Mortus Strider

When Mortus Strider dies, return it to its owner's hand.

Dream Fracture

Counter target spell. Its controller draws a card.
Draw a card.

Swamp

Phantom Ninja

Quickling

Flash (You may cast this spell any time you could cast an instant.)
Flying
When Quickling enters, sacrifice it unless you return another creature you control to its owner's hand.

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.

Disdainful Stroke

Counter target spell with mana value 4 or greater.

Frantic Search

Draw two cards, then discard two cards. Untap up to three lands.

Commander's Sphere

{T}: Add one mana of any color in your commander's color identity.
Sacrifice Commander's Sphere: Draw a card.

Negate

Dismal Backwater

Dismal Backwater enters tapped.
When Dismal Backwater enters, you gain 1 life.
{T}: Add {U} or {B}.

Tishana's Tidebinder

Flash
When Tishana's Tidebinder enters, counter up to one target activated or triggered ability. If an ability of an artifact, creature, or planeswalker is countered this way, that permanent loses all abilities for as long as Tishana's Tidebinder remains on the battlefield. (Mana abilities can't be targeted.)

Mortuary Mire

Mortuary Mire enters tapped.
When Mortuary Mire enters, you may put target creature card from your graveyard on top of your library.
{T}: Add {B}.

Mana Leak

Counter target spell unless its controller pays {3}.

Arcane Signet

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.)

Waterfront District

Waterfront District enters tapped.
{T}: Add {U} or {B}.
{2}{U}{B}, {T}, Sacrifice Waterfront District: 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.

Baleful Strix

Flying, deathtouch
When Baleful Strix enters, draw a card.

Mirage Mesa

Mirage Mesa enters tapped. As it enters, choose a color.
{T}: Add one mana of the chosen color.

Roaming Throne

Ward {2}
As Roaming Throne enters, choose a creature type.
Roaming Throne is the chosen type in addition to its other types.
If a triggered ability of another creature you control of the chosen type triggers, it triggers an additional time.

Siren of the Silent Song

Flying
Inspired — Whenever Siren of the Silent Song becomes untapped, each opponent discards a card, then each opponent mills a card.

Triton Shorestalker

Path of Ancestry

Path of Ancestry enters 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.)

Dimir Guildgate

Dimir Guildgate enters tapped.
{T}: Add {U} or {B}.

Fake Your Own Death

Until end of turn, target creature gets +2/+0 and gains "When this creature dies, return it to the battlefield tapped under its owner's control and you create a Treasure token." (It's an artifact with "{T}, Sacrifice this artifact: Add one mana of any color.")

Drowned Catacomb

Drowned Catacomb enters tapped unless you control an Island or a Swamp.
{T}: Add {U} or {B}.

Languish

All creatures get -4/-4 until end of turn.

Soured Springs

Soured Springs enters tapped.
When Soured Springs enters, it deals 1 damage to target opponent.
{T}: Add {U} or {B}.

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.