Ok I will give another clue for today, I honestly think that first clue was a bit misleading lol.
Clue 1: This character is only limbless in one game it's in.
Clue 1a: In other appearances this character has limbs.
Clue 2: This character was only in one mainline game.
Clue 3: This character has multiple of it.
Clue 4: This character is not organic.
Clue 4a: This character is literally not made out of organs.
Clue 5: They command to their leader who is a version of them.