Have

Smoke Shroud

Enchant creature
Enchanted creature gets +1/+1 and has flying.
When a Ninja enters the battlefield under your control, you may return Smoke Shroud from your graveyard to the battlefield attached to that creature.

Tormented Soul

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

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.

Levitation

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."

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.

Devastation Tide

Return all nonland permanents to their owners' hands.
Miracle {1}{U} (You may cast this card for its miracle cost when you draw it if it's the first card you drew this turn.)

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.

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.

Ponder

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

Swamp

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.

Rogue's Passage

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

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.

Swiftfoot Boots

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

Misdirection

You may exile a blue card from your hand rather than pay this spell's mana cost.
Change the target of target spell with a single target.

Kotose, the Silent Spider

When Kotose, the Silent Spider enters the battlefield, exile target card other than a basic land card from an opponent's graveyard. Search that player's graveyard, hand, and library for any number of cards with the same name as that card and exile them. Then that player shuffles. For as long as you control Kotose, you may play one of the exiled cards, and you may spend mana as though it were mana of any color to cast it.

Brainstorm

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

Erratic Portal

{1}, {T}: Return target creature to its owner's hand unless its controller pays {1}.

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.")

Thought Vessel

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

Mask of Riddles

Equipped creature has fear. (It can't be blocked except by artifact creatures and/or black creatures.)
Whenever equipped creature deals combat damage to a player, you may draw a card.
Equip {2}

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.

Triton Shorestalker

Otherworldly Gaze

Surveil 3. (Look at the top three cards of your library, then put any number of them into your graveyard and the rest on top of your library in any order.)
Flashback {1}{U} (You may cast this card from your graveyard for its flashback cost. Then exile it.)

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.

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.

Decanter of Endless Water

You have no maximum hand size.
{T}: Add one mana of any color.

Slither Blade

Changeling Outcast

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

Manifold Key

{1}, {T}: Untap another target artifact.
{3}, {T}: Target creature can't be blocked this turn.

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.

Key to the City

{T}, Discard a card: Up to one target creature can't be blocked this turn.
Whenever Key to the City becomes untapped, you may pay {2}. If you do, draw a card.

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.

Deadly Rollick

If you control a commander, you may cast this spell without paying its mana cost.
Exile target creature.

Cryptic Spires

As you create your deck, circle two of the colors below.
Cryptic Spires enters the battlefield tapped.
{T}: Add one mana of either of the circled colors.

Island

Deepchannel Mentor

Blue creatures you control can't be blocked.

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.

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.

Treasure Cruise

Delve (Each card you exile from your graveyard while casting this spell pays for {1}.)
Draw three cards.

Whispersilk Cloak

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

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.)

Tetsuko Umezawa, Fugitive

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

Reliquary Tower

Choked Estuary

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

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.

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.

Lost Vale

(Transforms from Dowsing Dagger.)
{T}: Add three mana of any one color.

Dowsing Dagger

When Dowsing Dagger enters the battlefield, target opponent creates two 0/2 green Plant creature tokens with defender.
Equipped creature gets +2/+1.
Whenever equipped creature deals combat damage to a player, you may transform Dowsing Dagger.
Equip {2}

Dowsing Dagger // Lost Vale

Kaito's Pursuit

Target player discards two cards. Ninjas and Rogues you control gain menace until end of turn. (They can't be blocked except by two or more creatures.)

Krydle of Baldur's Gate

Whenever Krydle of Baldur's Gate deals combat damage to a player, that player loses 1 life and mills a card, then you gain 1 life and scry 1.
Whenever you attack, you may pay {2}. If you do, target creature can't be blocked this turn.

Karn's Temporal Sundering

(You may cast a legendary sorcery only if you control a legendary creature or planeswalker.)
Target player takes an extra turn after this one. Return up to one target nonland permanent to its owner's hand. Exile Karn's Temporal Sundering.

Familiar's Ruse

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

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}.

Venser's Journal

You have no maximum hand size.
At the beginning of your upkeep, you gain 1 life for each card in your hand.

Vorpal Sword

Equipped creature gets +2/+0 and has deathtouch.
{5}{B}{B}{B}: Until end of turn, Vorpal Sword gains "Whenever equipped creature deals combat damage to a player, that player loses the game."
Equip {B}{B}

Counterspell

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.

Propaganda

Creatures can't attack you unless their controller pays {2} for each creature they control that's attacking you.

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.

Throatseeker

Unblocked attacking Ninjas you control have lifelink.

Time Warp

Target player takes an extra turn after this one.

Phantom Ninja

Flood of Tears

Return all nonland permanents to their owners' hands. If you return four or more nontoken permanents you control this way, you may put a permanent card from your hand onto the battlefield.

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.

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.)

Invisible Stalker

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

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.)

Perplex

Counter target spell unless its controller discards their hand.
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.)

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.

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.

Cunning Evasion

Whenever a creature you control becomes blocked, you may return it to its owner's hand.

Command Tower

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

Access Tunnel

{T}: Add {C}.
{3}, {T}: Target creature with power 3 or less can't be blocked this turn.

Temporal Mastery

Take an extra turn after this one. Exile Temporal Mastery.
Miracle {1}{U} (You may cast this card for its miracle cost when you draw it if it's the first card you drew this turn.)