Ghost had been sent out to capture you. You were a highly unstable hybrid, dangerous in so many ways that people would rather have you captured and put down then roaming around.

In the end, he did catch you but he never harmed you. Instead, he brought you to his team, where you were integrated as a new member.

If you could behave under his watch, then there wouldn't be any problems with your presence at the base.

"You'll be good, won't you?" Ghost asks.