In the absence of hard evidence, we can still fall back on the process of elimination. We eliminate the suspects one by one until someone starts confessing!
...No? F-Fine. Then, let me explain it this way.
We can eliminate
Spooks because the showers in the Decontamination Room struggle to clean hard surfaces like metal, so he would have no way to quickly clean blood off of his robotic body. Can he even fire a gun with those claws anyway?
Astrid supposedly spent a lot of time in only a couple of locations last night, but Beepy sees her shortly before getting into a firefight with the alleged murderer. The timing would have to be very tight for her to carry out the murder in the time that it took Beepy to lap the Historical Society.
Lyra was snoozing during the time of the murder, as logged by the equipment in the Sleep Lab. For the sake of simplicity, we should assume that not even she could use her expertise to fiddle with the readings in there.
Dexter couldn't have stolen Lyra's access card because she was awake at the time that she heard him rummaging through the toolkit in the Boiler Room. He would have no way of knowing when she'd fallen asleep, and Spooks saw him leave to the Lobby.
Nancy would have little opportunity to commit the murder in the time that she and Beepy were separated. It would also be pretty silly if she crossed the Facility Grounds on her way to wash herself off, knowing full well that her buddy was patrolling there.
Finally,
Beepy is the hero who got into a shootout with our villain! It would be difficult for him to fake being in two places at one to fire two different projectiles in different directions at roughly the same time. Maybe he's crazy fast, but if he was that strong, he wouldn't need to steal some old dagger to kill someone in the first place.
While we don't have any smoking gun, everything falls into place most snugly if we assume that
Gus is lying. He has a huge gap in his testimony after the last time he sees another person, he could easily lie about hearing gunshots if he was one of the shooters, the murder weapon was found with his belongings, and we're supposed to believe that he can fix a display case in a couple of minutes but has to spend a whole night fixing a fountain? Mr. Godbert could've handled it in a jiffy! Also, your mustache is way lamer than his!
Vote: Gus Odeon