Below are the side quests that can be obtained in the Central Factory!
Daring Assault (timed)
Obtained: Surprise Quest
Objective: Defeat the M96 Crisis Unit and 2 Crisis Response Units in the Mechon Factory
This quest will trigger when you head through the Mechon Factory on the 3rd floor. The M96 Crisis Unit is a level 61 enemy and the Crisis Response Units are level 60. Defeat them to complete the quest.
Eliminate the Backup! (timed)
Obtained: Surprise Quest
Objective: Defeat Beautiful Vagul in the Storage Depot
This quest will trigger when you approach the Storage Depot, which is on GF of the Central Factory. Beautiful Vagul is a level 60 unique enemy that is accompanied by 2 level 56 M57/BEASTs. There are other enemies that you can also pull as well in the Storage Depot. After defeating the unique enemy, the quest will complete.
New Weapon for Fiora (timed)
Obtained: Speak with the Junks Staff on Junks when the Junks ship lands at Central Factory
Objective: Use the Weapon Creation Machine in the Control Tower of the Central Factory
You will be able to reach this area after the story cutscene with Shulk deep in thought and Fiora tells him that he can tell her or the others anything. When you’re ready, head towards the Maintenance Wing on the ground floor. Interact with the machine in the middle of the room to complete the quest.