Constructing a Deck based around "Ninja" monsters is no simple feat, as they don't fight by conventional means; the Spell, Trap and Monster cards of the "Ninja" archetype revolve around underhanded, control-based strategies rather than all-out attacking or swarming.
Overall, "Ninja" Decks can be made in a variety of ways, but since Ninja-specific support is few and far in between, most of their abilities are far from game-breaking, making them more of an uncommon rogue Deck to use. However, they can excel against Stall Decks that revolve around a particular, titular card (Which "Ninja" are adept at destroying). The transformationtraps in their arsenal give "Ninja" splashability with "Mist Valley", "Chaos", "Dragon", "Dark Simorgh Lockdown" and "Monarch" Decks, among others.
To effectively play the Archetype, "Ninja" Duelists must consider a large variety of monsters. For example, WIND and/or Winged-Beast-oriented Decks aid "Lady Ninja Yae", while DARK monsters will keep up the stealth of "Strike Ninja". Others still, such as "Goe Goe" and "Ebisu", work better together than alone. Ideally, one should attempt to use monsters that fill several niches in one Deck; for example, "Dark Simorgh" is DARK, WIND and Winged-Beast, giving support to not only the above Ninja and "Hanzo", but is an ideal target for "Ninjitsu Art of Transformation". Continuing on this idea, "Roc from the Valley of Haze" can return to the Deck once he is discarded by "Yae" to become her transformation target within the same turn.
The age-old "Armed Ninja" and "Crimson Ninja" will be difficult to use in a Deck, as their effects are sub-par, and their low level makes them a less-than-ideal target for the transformation Traps; they instead are more useful when paired with such cards as "Ninjitsu Art of Duplication" and "Senior Silver Ninja", both of which enable the weak "Ninja" to swarm the Field, ready to Flip.
"White Dragon Ninja" is the strongest monster in this archetype and is meant to be paired with "Super-Transformation" by means of her own effect that protects the controlling player's back-row. This card has a strong synergy with the card "Safe Zone", due to it then being indestructable apart from being returned to the user's hand from an effect such as "Neo-Spacian Grand Mole". Some monsters, such as "Tyrant Dragon" and "Galaxy-Eyes Photon Dragon", also have means to bypass the debilitating effects of Super-Transformation.
There are ways to break the Safe Zone and White Dragon Ninja lock once it has been completed, such as using Trap Stun to temporarily remove Safe Zone's protection from White Dragon Ninja, using Trap Eater to remove Safe Zone (since it doesn't destroy), using Book of Eclipse to flip White Dragon Ninja face-down (since it doesn't target or destroy), both removing Safe Zone's protection and temporarily nullifying White Dragon Ninja's effect, or using Skill Drain.
Summon "Earth Armor Ninja" first, then use "Flame Armor Ninja" to increase the level of itself or another Level 4 "Ninja" monster by 1 for the Xyz Summon.
Summon "Earth Armor Ninja", then Tribute him to Set "Senior Silver Ninja". Either use "Book of Taiyou" or wait until he is flipped face-up. IF you used "Book of Taiyou", Special Summon "Earth Armor Ninja" and "Air Armor Ninja" and decrease the Level of "Senior Silver Ninja" by 1, bringing it down to 5 during your next turn or use card effects to flip them face-up.
"Upstart Golden Ninja" can trade your useless "Ninjitsu Art" or other Trap for a lesser "Ninja"; you could set "White Ninja" or "Sazank" for their Flip Effects, or Special Summon "Hanzo" face-up to thus profiteer off of his effect. Lastly, if the "Ninja" you summoned face-up is level 4, you can even overlay with "Upstart" for "Blade Armor Ninja".
"Goe Goe the Gallant Ninja" and "Ninja" in general get support in the form of "Masked Ninja Ebisu", who can send set Spell/Trap cards back to your opponent's hand for an safer and cleaner strike. "Goe Goe" can then attack directly via the effect of "Ebisu" (Twice directly if you use the effect of "Blade Armor Ninja" or multiple "Goe Goe"), and possibly discard cards from their hand, including ones sent back with "Ebisu".
Use "Lady Ninja Yae" to bounce your opponent's cards, and use "Goe Goe the Gallant Ninja" or "Masked Ninja Ebisu" to discard them. "Goe Goe the Gallant Ninja" or "Masked Ninja Ebisu" can also be used as the cost for this card.
Set-up your Pendulum Scales and Ninja Transformation plays. Ideally, you'll summon Apex Avian with Transformation. Apex can negate a card by returning itself to the hand, it makes the perfect monster for you to continuously Pendulum Summon every turn from your hand allowing you to negate 1 card every turn and also giving you a massive attacking body. Use its effect to negate something and Pendulum Summon it later. Backrow and draw power cards help. The decks primary offensive plays are Rank 4 Xyz Summons, Transformation and Pendulum Summons.
"Ninjitsu Art of Transformation", can be used by order to Special Summon "Dark Simorgh". Can be part of a lockdown: Use "Anti-Spell Fragrance" so that your opponent can't activate Spell Cards from their hand, nor activate them when on the field.
"Ninjitsu Art of Super-Transformation" can be used to take out one of your opponent's more troublesome monsters, and replace it with a stronger and more splashable monster of your own, such as 'Blue' or 'White' Dragon Ninja.
However, these Traps rely on the presence of at least one face-up "Ninja" on the Field; one must keep this in mind if they are planning to use a larger number of outsiders such as "Cyber Dragon" (Over "Earth Armor") and "Necro Gardna" (Over "Aqua Armor").
"Ninjitsu Art of Duplication" main use is for an OTK/Power play. Like Transformation, it can also be used to dodge targeting card effects and get rid of extra attacks.
"Ninjitsu Art of Shadow Sealing" just like the other previous ninjitsu art cards, this can be used to dodge targeting card effects. The difference, however, is instead of summoning a monster, you get to banish one of your opponent’s. This can be useful in addressing the deck’s weakness of spot removal. Many write off the card, but when using it in this fashion, it is actually a useful card that works out card advantage wise. Still, it's better as a side against Evilswarm and other XYZ reliant decks.