I thought it would be cool if Artie was the one actually stealing his own artifacts and that he had imagined that the Brotherhood was doing it. He was familiar with storage space where the rifle and other artifacts were stored, as he'd been there before. He put the astrolabe in the Dark Vault, where Alice's Mirror was stored before being stolen. Maybe his own paranoia/guilt is making him do these things without realizing and that's the "evil" that Brent Spiner's character was talking about.
At least, I thought that would be a cool way to go with the storyline. Whether they actually do something like that or not remains to be seen.