Possible situations on why William would show up next season
1. Brad gets arrested on an alien planet because they believe he's a spy for The Federation. They later realise that it was a case of mistaken identity, and discover William is alive and working for Section 31
2. Brad is silently replaced with William to carry out a mission on The Cerritos. The mission? Assassinating another character (there's apparently a murder mystery episode so ya know could be linked)
3. William replaces Brad for his own protection. Someone wants Brad dead, and Section 31 is aware, so send William to replace him and find the culprit
I think that clip from the teaser of T'Lyn, Jennifer, Mariner, Tendi and Rutherford running into that room looking pissed could be them trying to free Brad. Either from a prison he's held in on suspicion of being a spy, or from a Section 31 facility.
I want a shocking reveal towards the end of the season that Brad got replaced in, like, episode 3 or something.