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.)

Three Steps Ahead

Spree (Choose one or more additional costs.)
+ {1}{U} — Counter target spell.
+ {3} — Create a token that's a copy of target artifact or creature you control.
+ {2} — Draw two cards, then discard a card.

Turn Aside

Counter target spell that targets a permanent you control.

Ponder

Look at the top three cards of your library, then put them back in any order. You may shuffle.
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.)

Contaminated Aquifer

({T}: Add {U} or {B}.)
Contaminated Aquifer enters tapped.

Disdainful Stroke

Counter target spell with mana value 4 or greater.

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.")

Mind Stone

{T}: Add {C}.
{1}, {T}, Sacrifice Mind Stone: Draw a card.

Corrupted Conviction

As an additional cost to cast this spell, sacrifice a creature.
Draw two cards.

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.)

Village Rites

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.

Undercity Sewers

({T}: Add {U} or {B}.)
Undercity Sewers enters tapped.
When Undercity Sewers enters, surveil 1. (Look at the top card of your library. You may put it into your graveyard.)

Familiar's Ruse

As an additional cost to cast this spell, return a creature you control to its owner's hand.
Counter target spell.

Triton Shorestalker

Midnight Clock

{T}: Add {U}.
{2}{U}: Put an hour counter on Midnight Clock.
At the beginning of each upkeep, put an hour counter on Midnight Clock.
When the twelfth hour counter is put on Midnight Clock, shuffle your hand and graveyard into your library, then draw seven cards. Exile Midnight Clock.

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.

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.

Agent of the Shadow Thieves

Commander creatures you own have "Whenever this creature attacks a player, if no opponent has more life than that player, put a +1/+1 counter on this creature. It gains deathtouch and indestructible until end of turn."

Reflecting Pool

{T}: Add one mana of any type that a land you control could produce.

Counterspell

Archmage's Charm

Choose one —
• Counter target spell.
• Target player draws two cards.
• Gain control of target nonland permanent with mana value 1 or less.

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.

Tetsuko Umezawa, Fugitive

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

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.)

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.

Negate

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.

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.

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.)

Changeling Outcast

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

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.

Dimir Locket

{T}: Add {U} or {B}.
{U/B}{U/B}{U/B}{U/B}, {T}, Sacrifice Dimir Locket: Draw two cards.

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.

Unearth

Return target creature card with mana value 3 or less from your graveyard to the battlefield.
Cycling {2} ({2}, Discard this card: Draw a card.)

Dimir Aqueduct

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

Plaza of Heroes

{T}: Add {C}.
{T}: Add one mana of any color. Spend this mana only to cast a legendary spell.
{T}: Add one mana of any color among legendary permanents you control.
{3}, {T}, Exile Plaza of Heroes: Target legendary creature gains hexproof and indestructible until end of turn.

Morphic Pool

Morphic Pool enters tapped unless you have two or more opponents.
{T}: Add {U} or {B}.

Slither Blade

Thought Vessel

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

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.

Countersquall

Counter target noncreature spell. Its controller loses 2 life.

Flusterstorm

Counter target instant or sorcery spell unless its controller pays {1}.
Storm (When you cast this spell, copy it for each spell cast before it this turn. You may choose new targets for the copies.)

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.

Insatiable Avarice

Spree (Choose one or more additional costs.)
+ {2} — Search your library for a card, then shuffle and put that card on top.
+ {B}{B} — Target player draws three cards and loses 3 life.

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.

Consider

Surveil 1. (Look at the top card of your library. You may put it into your graveyard.)
Draw a card.

Sunken Hollow

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

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.

Miscast

Counter target instant or sorcery spell unless its controller pays {3}.

Keep Safe

Counter target spell that targets a permanent you control.
Draw a card.

Command Tower

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

Dimir Cluestone

{T}: Add {U} or {B}.
{U}{B}, {T}, Sacrifice Dimir Cluestone: Draw a card.

Brainstorm

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

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.

Swamp

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

Dispel

Scry 1. (Look at the top card of your library. You may put that card on the bottom.)
Draw a card.

An Offer You Can't Refuse

Counter target noncreature spell. Its controller creates two Treasure tokens. (They're artifacts with "{T}, Sacrifice this token: Add one mana of any color.")

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.

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.

Arcane Denial

Counter target spell. Its controller may draw up to two cards at the beginning of the next turn's upkeep.
You draw a card at the beginning of the next turn's upkeep.

Underground River

{T}: Add {C}.
{T}: Add {U} or {B}. Underground River deals 1 damage to you.

Island

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.

Envelop

Reanimate

Put target creature card from a graveyard onto the battlefield under your control. You lose life equal to its mana value.

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.

Coastal Piracy

Whenever a creature you control deals combat damage to an opponent, you may draw a card.

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.

Fetid Pools

({T}: Add {U} or {B}.)
Fetid Pools enters tapped.
Cycling {2} ({2}, Discard this card: Draw a card.)

Talisman of Dominance

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

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.

Dimir Signet

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.

Sol Ring

Invisible Stalker

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

Drowned Catacomb

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

Sunken Ruins

{T}: Add {C}.
{U/B}, {T}: Add {U}{U}, {U}{B}, or {B}{B}.

Choked Estuary

As Choked Estuary enters, you may reveal an Island or Swamp card from your hand. If you don't, Choked Estuary enters tapped.
{T}: Add {U} or {B}.

Zareth San, the Trickster

Flash
{2}{U}{B}, Return an unblocked attacking Rogue you control to its owner's hand: Put Zareth San, the Trickster from your hand onto the battlefield tapped and attacking.
Whenever Zareth San deals combat damage to a player, you may put target permanent card from that player's graveyard onto the battlefield under your control.

Darkwater Catacombs

Watery Grave

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