“Trees Made of Glass: Part 2” is episode two of season one of Threshold.
The freighter that was found in the previous episode, “Trees Made of Glass: Part 1”, was a Naval freighter, which explains the confusion over whether it was military or civilian. The sole crew member who was found alive jumped off the shop even after being shot four times.
Caffrey and Cavennaugh, who had watched, along with Lucas, the video of the alien incursion, had had the same dream, about the titular trees made of glass, which the captain of the freighter had also had visions of. When Caffrey got up, she found Gunneson, the mate of the freighter who had jumped overboard, standing next to her, despite being shot, his ship being scuttled, and being many miles out to sea. Gunneson attacks her, but is driven off and vanishes.
Dr Fenway is examining the living things found on the ship, some of which are mutating, and the dead crewmen. With Gunneson ashore, that suggests that the other missing crew members may have made it too, so the search is on for them. It isn’t known whether they are infectious or not, or what truly is happening to them, but they need containing.
Fenway hasn’t found anything physically wrong with Caffrey, Cavennaugh or Lucas, but the video has affected them to some degree. Lucas and Fenway are also looking into how the video affects living beings.