Mysterious and shadowy, Ninja continue to be almost as much of a mystery to the average SeeD as they are to everyone else on the planet. There are only three Ninja in SeeD at the moment, all three of them having passed an Exam. The origen of this archetype in the organization is also shrouded in mystery. A contract, between Squall and the Ninja clan, shortly after his insane rage and destruction of a rouge Ninja fortress, provided for the three Ninjas that joined SeeD five years ago. Now, those three make their way in a confusing world, made more confusing by a memory seal designed to protect them from those that seek the clan's secrets.

SeeD doesn't really seem to know what to do with the Ninja at the moment, they've been deployed to squads lead by young officers, presumably as infiltrators superior to the Rouges. So far there seems to be no prejudice against the Ninja from within SeeD itself, even among Samurai SeeDs. After all, the SeeD samurai are obviously not fulfilling a totally traditional path either.

Ninja can, at least as far as has been revealed so far, inflict a variety of supernatural venoms on their foes. They also seem to have a great deal of control over darkness elemental magic, something SeeD as a whole is barely familier with. Finally, there are no finer infiltrators than a Ninja. As politics and power struggles become more complex in Gaia, there will doubtless be need for those who can enter a secure area, perform some operation, and exit without ever being detected. It seems that task will fall to the Ninja, though if the clan has any plans to send more trainees now that the first three have proved themselves is unknown.