NieR:Automata Ver1.1a Part 2 Episode 4

The machine lifeforms not only infected the YoRHa soldier units on the ground, they also infected the with a viral attack, activating a self-destruct sequence.

With this, the 13th Orbital Satellite Base was destroyed.

2B and 9S avoided infection from the virus and escaped the Bunker before it was destroyed.
Proposal: Find the remaining surviving YoRHa Soldiers and start another descent-to-ground operation on Earth to fulfill the mission.