Resistance Camp
After The Machine Surge
After Machine Recon
Storage area
Available after completing The Manager's Request.
After Assault
After The Forest Kingdom
Emil's shop
You must have talked to him at the entrance to the desert at least once for his routes to vary. When stopped in front of Resistance Camp, Emil sells either +6 chips or weapons, semi-rare materials and a Dress Module. Keep reloading the area if he doesn't show up or if he's not selling what you're looking for.
After Missile Supply Mission
There is now a shop selling unique chips, including Auto-collect Items.
After Resupply
Once you talk to Anemone, you are at the last point in the playthrough where you have access to the open world, quests, items, etc. Anything optional you still want to do on this playthrough, do it before heading to Abandoned Factory.
During Weird Machines
Route C
Pearl Harbor documents
Keep talking to Anemone until she tells you to examine the computer.