There was a break-in at Central Command two nights ago.
Everything has the look of being done by someone who's memorized the layout of our base at Central Command, but didn't have a lot of technical knowledge. The science geeks noticed a lot of stuff on their computers was accessed, which means whoever was responsible wasn't exactly concerned with covering their tracks. Security camera footage was wiped for that entire evening all across the base, though, so we have absolutely no idea who it actually was. Guards are well-trained and know how to handle stuff like this, but they didn't spot anybody.
Which means the intruder had someone on the inside at Central Command to wipe the footage and avoid raising the alarm, while maintaining a solid body count of zero. They've already apprehended everyone involved on the night shift for interrogation. Apparently, all the files accessed on the computers had to do with paranormal activity relating to temporal manipulation, and dimensional theory. In other words, time control and knowledge on alternate dimensions. This may not even be related to the situation with B2, but it'd add up with his recent disappearance, freak-out, and knowledge of the base's layout. Plus, snipers are supposed to avoid detection, so, his infiltration training would help.
Still checking out multiple leads. So far, nothing.
But if it's B2, why would he go for information on time travel or alternate dimensions? Slender Man related? Most likely.