Brotherhood Regalia

Equipped creature has ward {2}, is an Assassin in addition to its other types, and can't be blocked.
Equip legendary creature {1}
Equip {3} ({3}: Attach to target creature you control. Equip only as a sorcery.)

Underground River

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

Spectral Sailor

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

Vampiric Tutor

Search your library for a card, then shuffle and put that card on top. You lose 2 life.

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.

Opposition Agent

Flash
You control your opponents while they're searching their libraries.
While an opponent is searching their library, they exile each card they find. You may play those cards for as long as they remain exiled, and you may spend mana as though it were mana of any color to cast them.

Arcane Signet

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

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.

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

Rogue's Passage

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

Mystic Sanctuary

({T}: Add {U}.)
Mystic Sanctuary enters tapped unless you control three or more other Islands.
When Mystic Sanctuary enters untapped, you may put target instant or sorcery card from your graveyard on top of your library.

Sunken Hollow

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

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.

Reliquary Tower

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

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.

Triton Shorestalker

Deadly Rollick

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

Baleful Strix

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

Rivendell

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

Nanogene Conversion

Choose target creature you control. Each other creature becomes a copy of that creature until end of turn, except it isn't legendary.

Eagle Vision

Freerunning {1}{U} (You may cast this spell for its freerunning cost if you dealt combat damage to a player this turn with an Assassin or commander.)
Draw three cards.

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.)

Swamp

Ogre Slumlord

Whenever another nontoken creature dies, you may create a 1/1 black Rat creature token.
Rats you control have deathtouch.

Ingenious Prodigy

Skulk (This creature can't be blocked by creatures with greater power.)
Ingenious Prodigy enters 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.

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.

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.)

Bojuka Bog

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

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.

Tetsuko Umezawa, Fugitive

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

Propaganda

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

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.

Soporific Springs

As Soporific Springs enters, you may pay 3 life. If you don't, it enters tapped.
{T}: Add {U}.

Sink into Stupor

Return target spell or nonland permanent an opponent controls to its owner's hand.

Sink into Stupor // Soporific Springs

Smoke Bomb

Flash
All creatures have shroud. (They can't be the targets of spells or abilities.)
At the beginning of your upkeep, sacrifice Smoke Bomb. When you do, target creature you control can't be blocked this turn.

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."

Counterspell

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.)

Access Tunnel

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

Changeling Outcast

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

Negate

Faerie Seer

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.

Dig Through Time

Delve (Each card you exile from your graveyard while casting this spell pays for {1}.)
Look at the top seven cards of your library. Put two of them into your hand and the rest on the bottom of your library in any order.

Gingerbrute

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

Slither Blade

Maskwood Nexus

Creatures you control are every creature type. The same is true for creature spells you control and creature cards you own that aren't on the battlefield.
{3}, {T}: Create a 2/2 blue Shapeshifter creature token with changeling. (It is every creature type.)

Faerie Dreamthief

Flying
When Faerie Dreamthief enters, surveil 1. (Look at the top card of your library. You may put it into your graveyard.)
{2}{B}, Exile Faerie Dreamthief from your graveyard: You draw a card and you lose 1 life.

Brainstorm

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

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.

Flare of Denial

You may sacrifice a nontoken blue creature rather than pay this spell's mana cost.
Counter target spell.

Sol Ring

Ponder

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

Halimar Depths

Halimar Depths enters tapped.
When Halimar Depths enters, look at the top three cards of your library, then put them back in any order.
{T}: Add {U}.

Snarling Gorehound

Menace
Whenever another creature you control with power 2 or less enters, surveil 1. (Look at the top card of your library. You may put it into your graveyard.)