Hero's Blade

Equipped creature gets +3/+2.
Whenever a legendary creature you control enters, you may attach Hero's Blade to it.
Equip {4} ({4}: Attach to target creature you control. Equip only as a sorcery.)

Ornithopter

Gingerbrute

Haste (This creature can attack and {T} as soon as it comes under your control.)
{1}: Gingerbrute can't be blocked this turn except by creatures with haste.
{2}, {T}, Sacrifice Gingerbrute: You gain 3 life.

Whispersilk Cloak

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

Changeling Outcast

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

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}.

Rogue's Passage

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

Artful Dodge

Target creature can't be blocked this turn.
Flashback {U} (You may cast this card from your graveyard for its flashback cost. Then exile it.)

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.

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.

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.)

Have

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.

Cliffhaven Kitesail

When Cliffhaven Kitesail enters, attach it to target creature you control.
Equipped creature has flying.
Equip {2} ({2}: Attach to target creature you control. Equip only as a sorcery.)

Sai of the Shinobi

Equipped creature gets +1/+1.
Whenever a creature you control enters, you may attach Sai of the Shinobi to it.
Equip {2}

Neko-Te

Whenever equipped creature deals damage to a creature, tap that creature. That creature doesn't untap during its controller's untap step for as long as Neko-Te remains on the battlefield.
Whenever equipped creature deals damage to a player, that player loses 1 life.
Equip {2}

Hankyu

Equipped creature has "{T}: Put an aim counter on Hankyu" and "{T}, Remove all aim counters from Hankyu: This creature deals damage to any target equal to the number of aim counters removed this way."
Equip {4} ({4}: Attach to target creature you control. Equip only as a sorcery.)

Eater of Virtue

Whenever equipped creature dies, exile it.
Equipped creature gets +2/+0.
As long as a card exiled with Eater of Virtue has flying, equipped creature has flying. The same is true for first strike, double strike, deathtouch, haste, hexproof, indestructible, lifelink, menace, protection, reach, trample, and vigilance.
Equip {1}

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.

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.

Baleful Strix

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

Manriki-Gusari

Equipped creature gets +1/+2 and has "{T}: Destroy target Equipment."
Equip {1} ({1}: Attach to target creature you control. Equip only as a sorcery.)

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.

Phantom Ninja

Tormented Soul

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

Invisible Stalker

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

Throatseeker

Unblocked attacking Ninjas you control have lifelink.

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's Kunai

Equipped creature has "{1}, {T}, Sacrifice Ninja's Kunai: Ninja's Kunai deals 3 damage to any target."
Equip {1} ({1}: Attach to target creature you control. Equip only as a sorcery.)

Blinding Powder

Equipped creature has "Unattach Blinding Powder: Prevent all combat damage that would be dealt to this creature this turn."
Equip {2} ({2}: Attach to target creature you control. Equip only as a sorcery.)

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."

Isochron Scepter

Imprint — When Isochron Scepter enters, you may exile an instant card with mana value 2 or less from your hand.
{2}, {T}: You may copy the exiled card. If you do, you may cast the copy without paying its mana cost.