I find it highly probable that 9S will become infected with the Bio-machine Logic Virus like we’ve seen in the YoRHa stage play.
This virus is gradual but will eventually take control of the android’s body, causing a typical “Berserk” sort of status effect. There is no known cure for this virus…therefore, in order to protect the remaining, uninfected androids… the infected units must be destroyed on the spot– no question.
It could be that 9S was infected during the opera boss battle that we saw in the E3 2016 trailer and only began to show symptoms or paralysis (possibly the first signs of a viral infection) after the fight when they were about to return to the Bunker. In the close up shot of 9S, he seemingly says “It’s useless” or “dame da” in Japanese…
Or he could have been infected long before meeting up with 2B since he was already on the surface of the planet doing recon work in preparation for the arrival of 2B’s squadron. I’ve already discussed the material from the script that was artistically shown during the character introduction trailer that was first shown at the NieR Music Concert & Talk Live. You can read more about that here.
Maybe this is why 2B seems very reluctant on leaving him or rather… having to kill him herself right then and there. If so, then perhaps 9S will take up a similar role like Yonah in the previous game. Maybe both 2B and 9S will hide the fact that he’s infected in order to somehow find a cure to save him.
Whether or not this all means that he will most certainly DIE at the end of the game is unknown.