I'm at the part where Jean-Baptiste wants me to bring Cass over to him, problem is, when I was last at the Mojave Outpost I killed a lot of the NCR because I wanted to make enemies with them.
When I told her that Baptiste wanted to speak with her she said she didn't mind, but she doesn't follow me.
I asked her if she wanted to come to free-side and she started to talk about papers.

Any idea how I can get her to leave that chair she seems superglued to and tag along with me on the quest?

You'll need to do the first quest for Alice McLafferty/Crimson Caravan's, which is delivering a holotape or something to Doctor Hildern at Camp McCarren. After you do that, you should be able to get another quest from Alice, about convincing Cass to sell her company. Then you'll just need to convince Cass to sell, and ask her to come with you.