For me right after I got Legion there was a discussion about wheather or not to sell him to Cerberus. I said I wanted to talk to him first, so I went downstairs and woke him up. I was able to get his side mission right away after talking with him. The IFF wasn't ready yet, so I went and did his mission. When I came back it was ready. All crew saved, all party members saved with max loyalty. So Idkmybff jill.
I did this exact same thing in my game, but when I went to do the next mission, Joker told me to take the shuttle instead.