After relocating to a new home office in Queens, the Alpha Team is settling in-well, for the most part. Meanwhile, across town, a confrontation on a train leads to murder. It isn't long before Wilson is on the phone to Dr. Rosen with a new assignment.
Turns out it's not just this train that's unusual- four trains in various parts of the country have had extreme incidents, adding up to five fatalities. Wilson thinks this could be an Alpha at work and wants Dr. Rosen to find the culprit. Fast.
Based on Rachel's assessment of the crime scene, Rosen thinks the Alpha in question is able to fire off bursts of pheromones when he or she feels threatened in order to cause mayhem. After taking a look at the surveillance tape, the team finds the Alpha they are looking for; A 17 year-old woman named Tracy Beaumont.
Working from home because the buzzing of the microwave tower across the street from the new office distracts him, Gary is able to locate Ms. Beaumont and Dr. Rosen calls in the team. This call is just in the nick of time for Rachel whose parents are trying to marry her off-seemingly by the end of the night. When the team spots Beaumont, she sees them too and ducks into a youth hostel. Immediately, her pheromones cause a riot in the building.
Tracy gets away but the team is able to catch her brother, Matthew, who seems to be aware of, but immune to Tracy's powers. Back at headquarters, Rosen gets Matthew to open up about himself and his sister, whose real name is Alice, but when Wilson shows up, his aggressive demeanor makes Matthew feel threatened and we find out that it is Matthew who shoots pheromones, not Alice. Bedlam ensues and Matthew is able to get away in the confusion but Wilson isn't so lucky: He gets pummeled to death. The team also discovers that the woman Matthew has been seen with isn't his sister at all. Alice is dead, probably the victim of Matthew's powers.
Before the melee, Gary was able to learn that Alice had recently purchased a bus ticket to Chicago. It makes sense for them to reacquire Matthew there. At the bus stop, Matthew professes his love to his girlfriend Tracy, the only person he knows isn't affected by his power, but when he finds out that she's been running from him all along, he gets angry and uses his power to cause a riot and flees the scene Bill, the only Alpha member who isn't affected by Matthew's power, catches Matthew and knocks him out cold. Meanwhile, Hicks who manages to fight off Matthew's power by use of a serotonin shot, is able to save Tracy's life.
With Matthew safely secured at Binghamton Special Research Facility and his ex-girlfriend safe from harm, the team is left to ponder what will become of them now that Wilson, their DOD handler, is dead. Ironically, Gary and Hicks, the two team-members who had the most trouble adjusting, are the two who are least worried. Especially after Hicks fixes the humming only Gary can hear.