Worst case scenario expert, Dr. Caffrey, recruits a team of elite and slightly eccentric scientists to determine if an alien civilization has made first contact with the human race. Mysteries abound. Is the alien race trans-dimensional? Is it friendly or malevolent? If friendly, why did the crew members of the ship that encountered the alien kill each other? Is the strange helical symbol an attempt at communication? Are the aliens altering the DNA of human test subjects? And how are the odd dreams/nightmares everyone is having related?
At least one, and possibly seven, individuals from the ill fated Big Horn have survived but have disappeared. One in particular tends to reappear to menace but also possibly to communicate with Dr. Caffrey, then vanish just as suddenly. The team plans to capture the missing sailors with an audio segment from a video of the alien encounter which attracts rats found on the Big Horn. But with such limited testing there is no telling who, or what, might show up.
As the Threshold team tracks down the source of an infection and another member succumbs to it, the team chaffs under the pressure of their jobs. It becomes clear that Threshold will have to expand substantially to contain the infection but tidbits of information begin to suggest they may be fighting for the wrong outcome.