Contains spoilers. You've been warned.

As per the events of the 2017 Midseason finale of the parent show, Tom is dead. Yesterday, the show came back. Liz decided to go on a sort of pilgrimage to mourn. She decided to leave Agnes in the care of...none other than Scottie Hargrave. We find out through dialogue that Tom testified for Scottie against his father, and that's how she's free.

So...that's that. Neither Halcyon nor Whitehall nor anything else from the spinoff was mentioned, but...I guess its safe to assume they are back on track just minus Tom and Howard. We'll just...never see it.