>I read th walkthrough's and I want to save everyone and have
>loyalty from everybody.
>
>I haven't done all the loyalty missions and I'm gonna clear
>those up before I find the iff and legion.
>
>if I do legion's loyalty mission after that, does that mean
>I'll lose some of the crew at the end?
>

You can only do Legion's loyalty mission. You can't do anything else, not going to the citidal, illium, omega, not one other mission other than Legion's loyalty mission. Once you do his loyalty mission, you must immediately use the IFF.