With everyone taking a break, it's revealed that Shulk will have a weapon just like the Monado made from Mechon engineering. You control Melia at the moment. You'll find Fiora at the pod depot south of the colony. After a cutscene revealing her need to stay with Shulk, an alarm goes off. You and Fiora have to go all the way to where the Junk inside Colony 6.
Your team will be back together minus Shulk. Go to the front of Colony 6 for a few battles. On the second and third battle, Shulk will be back in full form again. Do your best battling a few more major Telethias before the storm ends.
Clear out anymore sidequests before talking to Miqol again. Also if you can, continue rebuilding Colony 6 so your team experience would be higher and more prepared than before.