The first 5 low level command missions are easy enough to knock out quickly with your squadron. If you tried a couple in the past but can't remember which you've already done, a green check mark will appear over the instance image in the mission list if you've done it. I discovered I had already completed 4 different command missions so I just needed to do the 5th.

Once you have the 5 completed, a quest for the flagged mission will show up.