In Mass effect 2 if I do Legions Mission after the final mission, will it count in ME3?

In Me2, I was playing through again, and everytime I get legion, as soon as I try to go to another destination, it forces me to activate the IFF. So after that the crew is kidnapped, and I still haven't gone anywhere. So I know if you go to any other place in between when the IFF is activated, and the last Mission, Kelly gets grinded down, and killed. So i didn't want anyone dying so, before even activating Legion I went straight to collector base. Then after beating that mission i activated Legion, with everyone still alive and completed his mission. So i was wondering, since on Legions mission you make a pretty important choice, is that choice still going to carry on to ME3? I know it probably will, but I just want to make sure.