AE:Ninja
The basic idea for the Ninja is that they're androids similar to the ones in operation at the ACC (CHAPTER 08 . AN INNOCENT LIFE). This is not very consistent with early concept art (which paints the Ninja as largely human), but fits in well with Oni's final content (the WCG's "ninjabots" have the same breathing sounds as the Ninja, the Ninja say "robotic" things like "Sound detected", etc).
Like regulation androids, Ninja often operate in cooperative groups. Unlike regulation androids, Ninja operate far away from their "base", so they must carry their own emitters to stay connected. One idea is that certain Ninja classes have a set of powerful antennas. Those Ninja centralize the awareness on the level of the platoon, and relay the info to and from a higher level of command.
Platoons of Ninja can be coordinated on-site by a Comguy, but that's not necessary. What matters is that the ninjas of a same platoon can be assigned the same alarm group ID. If a Ninja engages the player and the platoon's "antenna ninja" is still alive, then the whole platoon will be notified of the player's whereabouts. If the antenna ninja is dead, there will be no such notification.
Another role of the Ninja is to eliminate rogue elements of the Syndicate on behalf of Mukade. It's not obvious what kind of situation could hint at that plotwise without altering the original missions too much. The most dramatic hint would be in CHAPTER 10 . CAT AND MOUSE, with Ninja systematically eliminating all the Strikers that Konoko leaves behind, to make sure there are absolutely no human witnesses.