Tom is jealous of Kyra because she and Alex share the Point Blanc connection that he’s been trying without success to get Alex to open up about; his lifelong best friend, ever since the events of season 1.
Think of the frustration. Your friend returns a completely changed person, haunted with something you’ve not seen or experienced in order to help him. And I think that’s the core of Tom’s issue: he feel useless, unable to help Alex with what he’s going through. He’s trying to come to terms with the fact that Alex is now of a new, strange world and he, Tom, doesn’t belong in it.
So when Kyra shows up and Alex finally gets relief and a person to actually recount the events of Point Blanc with, and sort of fork through the murk of it all, Tom feels dejected, useless and unwanted. Left out and like he doesn’t fit in. Like he can’t do anything to help, at least not enough.
That’s why he ends up lashing out at Kyra and being super protective of his friendship with Alex. I’m glad that in the end he realized he’s still valuable.
The endless cycle of complaining you’ve run out of fics to read, devouring the new 10-20k at the top of the date updated page and going back to complaining how you’ve run out of fics to read.
