The threshold team had been rounding up people who were infected previously by the food supply. The estimated about 200 people were infected.
The doctor announced the pregnant infectee was about to deliver the baby.
One person disappeared who was infected by the food (a chef) was tracked to a small town of 50 called Allenville. The Threshold team lost contact with their agents following him in Allenville.
They couldn't understand why he would go to such a small town since the infectee's want to infect as many people as possible. Checking the family history of the chef they found out his brother an MIT professor has a second home in allenville. The brother is a brilliant physicist.
Molly and Cavanough go to allenville posing as husband and wife, and the rest of the team stays in threshold headquarters to deal with the upcoming baby.
Molly and Cavanough reach allenville and go to the vans gps coordinates where the threshold team that went quiet was. When they got there they saw a woman shoving a human body into a wood shredder. They shot her and she leaned into the shredder as she was passing out.
They headed to the town to look for a phone since neither their cells or satellite phones were working. In town they went to a restaurant and soon determined that the residents of allenville were all infected. Everyone was eating huge raw steaks and protein drinks. Since Molly and Cavanough were partially exposed to the alien virus the town infectees were not aware they were not fully infected. They were given huge raw steaks and drinks and figured they better keep up the impression they were infected.
Cavanough ate almost the entire raw steak he was given, Molly had to say she just ate one a bit ago, since she couldn't touch hers.
Molly and Cavanough went to the professors house and found his house caretaker who communicated that the area was a great place and they were away from the Threshold team. (The infectees were aware of the Threshold group since Cavanoughs brother was infected and made his way to Allenville).
After the caretaker left the house they went back in and found some evidence that led them to a abandoned horse stable. They went to investigate and saw many townspeople led by the professor building something. It appeared to be something to communicate the alien signal to the masses via some mechanism..
Molly and Cavanough went back to town and looked to build some homemade bombs to destroy this device before it was completed. While at a grocery store Molly was able to find a land line that worked. While she was being watched by town infectees she called Threshold (under the guise of calling her uncle) and told them she reached allenville and it was everything they could believe, and all the people were great, the kind of people they were looking for, and they should come here as soon as possible.
Molly and Cavanough then went and snuck back to the horse stable. Cavanough planted his homemade bombs in various places. He heard the professor talking to another infectee that the device the were building was going to send a message to the aliens in outerspace. He said instead of taking years it would take hours since it was using tachyon signals. The device was going to be ready in a day.
As they were leaving the area near the stable, Cavanough and Molly were caught by Cavanoughs infected brother. Molly was able to shoot him to disable him. Cavanough wanted to kill him, but Molly said they should bring him along. Other infectees started chasing them. Initially Cavanough tried to carry his brother on his shoulder and run from them, but that was slowing them down. So they dumped him and kept running.
They eventually were forced back towards town where they discovered Threshold team members (lots of army guys led by the guy that plays her boss). They captured the town members and headed back to Threshold headquarters.
While the above story was happening it was mixed in with the delivery of the baby.
The baby was basically born and was tested as human. They took the baby away from the infected mother (who immediately wanted to breast feed it). She became very upset and broke free. She knocked the doctor out and was heading after her baby.
The two geek team members (midget and nerdy genius who was partially infected) were trying to hang on to the baby and evade her. Although she was always following them. They determined it was because the one nerdy genius was partially infected like Molly and Cavanough and the mother was tracking him instead of the baby. They tricked her by the midget taking the baby while the mother tracked the other guy (still carrying the baby blanket). She caught up with him and he opened the blanked to show one of his shoes and no baby.
The mother was furious and said she was going to kill him, he turned off the main power to threshold to try to evade her. Emergency power came on in a few seconds and he was running away when the doctor and him collided. The doctor had just woke up and was heading to help. The doctor was able to shoot the mother and disable her.
At the end the entire threshold team was together. The doctor informed them the baby was fine and human, but the mothers breast milk was infected and would surely infect the baby.
They captured everyone in allenville except cavanoughs brother who escaped.
They determined that the signal they were going to send to the aliens were coordinates for another alien ship to come to. The coordinates were two hundred meters above Washington DC.
The next scene showed the doctor walking the empty halls of Threshold. She saw the babies crib with no baby in it. She turned around to see a boy around 8 years old. He informed her he was born at Threshold. She determined he was the baby grown up. He said he wasn't alien and she saved him, and that her plan saved everyone. She asked if it would happen soon, and he said no it would take some time, and she wouldn't be around to see it. She said that was ok and hugged him. Then she woke up, content that her plan might just work.
Not the greatest ending for a series, but since it wasn't planned, it will have to do.
