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With Mary and the Army closing in on them, Charlie, Lisa and Allie return to the Clarke's farm in Lubbock where it all started. Allie is forced to make the most difficult decision of their lives.
Mary enters the UFO to finds some answers. The next day Allie escapes from the army with her parents and goes on the run with them. While waiting for help from Lisa's uncle Tom, the family is joined by John.
Mary and Dr. Wakeman get Allie, but Mary is freezed out by General Beers. Allie is taken to North Dakota and used as bait for the aliens. Lisa and Charlie go after them to get Allie back.
Charlie and Lisa learn about their daughter Allie's amazing powers while trapped in a perilous situation. Mary Crawford lays the groundwork to snatch the child for government research.
The next generation comes into play, as the children of both Jacob Clarke and Jesse Keys become the focus of both a government investigation and alien interest.
Eric Crawford continues his father's secret government investigation and pursues Jacob Clarke and Jesse Keys for answers about the existence of aliens.
The sins of the father come to light when Owen Crawford's sons take opposite positions on their father's secret government project. 1970: Col. Owen Crawford's sons Eric and Sam rally around their father after his career falls into shambles, but both boys have hidden agendas. An investigation takes Sam to Alaska, where he finds a new truth about the aliens that has dangerous consequences. Meanwhile, an adult Jesse Keys has returned from Vietnam as a drug addict who is haunted by his past.
In 1962, Col. Crawford given one month to find proof that the aliens are a danger to America. Marty and Howard went in search of Jacob Clarke. Jesse talks Russell into seeking help from the Air Force, to stop the aliens.
Years after Russell Keys left his family, he saw his son Jesse on the UFO. When it was over, Russell went to see his son, but his mother and her husband would not let him. Jesse sneaks out and joins Russell on the road. In Roswell, Col. Owen Crawford has been failing in his mission to discover the secret behind the alien spacecraft he found 10 years earlier. Owen goes undercover to find out the Clarke family secret before the project is shut down.
Capt. Russell Keys is in the midst of a dogfight over Germany during World War II when his plane becomes enveloped in a mysterious blue light, saving him and his crew of nine men from certain death. However, none of them have any real memory of what truly happened or how they survived. After the war, Russell tries to return to normal, only to be troubled by bizarre nightmares and headaches. He learns that every other crewmember on his mission has died mysteriously, and feels compelled to begin his own quest for answers. Meanwhile, the unscrupulous Capt. Owen Crawford uses anybody and any thing to be put in control of the crash alien ship. A mysterious stranger named John comes into the Clarke family life and leaves, just as Capt. Crawford suspects him from being escaped alien.
