She was on the Shenzhou, where the ship was lost. I had assumed that that was where her injury came from, AND why she was so much more standoffish to Michael... Essentially, she was the root cause of her losing her captain, her ship and her senses.

The loss of android lady also hit her hard in the fight against Control, as she has an AI implant in her head, and she could have been susceptible to it too! There's a lot of nuanced character development that is shown, not told.