The joke of the comic, as it also turns out, is that the two Cueballs dressed up as ninjas were just out to have a fun time teasing Stallman, and they seemed to know that Stallman's paranoia about Microsoft makes him sleep with no fewer than two katana swords near his bed. This type of sword was one of the traditionally made Japanese swords that were used by the samurai of feudal Japan mainly as a sidearm. A ninja or more accurately a Shinobi no mono was basically special forces in feudal Japan. They specialized in espionage, sabatoge, etc. they were a rough combination of MI6, CIA, and Navy SEAL in feudal japan. Although they did not specialize in assassinations, that is something that they could do. Although samurai could also be shinobi/ninjas if they chose to do that job, samurai is a social class while shinobi no mono/ninjas were a job, not a social class. So this makes sense in this comic with Stallman, the samurai, and the ninjas, the lackeys of the oppressing Microsoft (at least in his mind). It also turns out that they specifically choose targets for their raids who have reason to be paranoid of larger companies that might send someone after them, and thus sleep with weapons near their beds. Stallman has received a Katana due to this comic (see the trivia section).

If explaining a joke "kills" it, this violates every single article of the Geneva Convention, and then goes on to commit acts of war so indescribably inhumane that the authors never even considered them (lest their tongues burst into flame on the spot).

Jokes aside, I love ExplainXKCD and have had to check it more times than I'd like to admit.