Malcolm had it all for a moment, working a steady job with Jeri and finding love with Zaya. But Jeri's defence for a mass murderer crosses the line for him, so he quits (slash gets fired). He ends up helping Erik's sister Berry, and a brief moment of indiscretion with her contributes to his relationship with Zaya further fraying. They break up, and when retrieving her things, Zaya sees Berry. Awkward.
But it's not all shambles for Malcolm. Jessica hands him the keys to Alias Investigations just before she sets off for Mexico. We don't think he'll be helming Alias alone for too long, though.