Items can be found through the various areas of Sudra, sometimes out in the open and sometimes hidden in secret locations. After finding all Items in an area, a small yellow dot will appear in the upper-right corner of the in-game map for that area.
Some "commented out" dialog in the data files mentions that the icons Trace picks up for weapons and upgrades are actually program disks for the Axiom Disruptor, some of which may have been built by Athetos, but not all, and that the Axiom Disruptor and the disks were built by ancient Sudrans for their sudran soldiers before Trace Prime/Athetos arrived at Sudra.
Dialog by Trace after acquiring the Drill (Between cutscene 4 and 5):
"Another disk; must be the drill that disembodied voice was telling me to find. Where did she go?"
A note from Tom to himself during the Power Filter conversation between Elsenova and Trace (cutscene 11):
Note to self: The upgrades Trace finds should be programs made for Watchers by the Primordials. Mayber Athetos made some as well, but not all.