Episode One: Beyond the Sky
In 1944, there is an air battle in World War II, which is where we first see Captain Russell Keys. Suddenly strange lights appear, flying all around the planes. Then the opening credits happen, after which we flash forward to 1945, when Russell returns home from the war. Soon after that, the story flashes forward to 1947. We meet Captain Owen Crawford (Joel Gretsch), an intelligence officer who receives reports involving flying saucers. He has a couple of subordinates, Lt. Howard Bowen (Jason Gray-Stanford, whom I'd later see in Monk) and Lt. Marty Erickson. We also meet Owen's girlfriend, Sue, who witnesses a UFO crash near Roswell, New Mexico, and explores the debris, finding a piece of alien metal, which she takes with her. She is observed by an alien. Later, Owen is shown a crashed saucer by a man and his kids, who had found it in the wilderness. His superior, Colonel Thomas Campbell, oversees the military coverup of the crash, and freezes Owen out of the project. But Owen realizes one of the aliens from the saucer is missing (there were four bodies but five seats in the ship), and he wants to find the living one.

Meanwhile, Russell is married to a woman named Kate (Julie Benz) and they have a baby son named Jesse. Russell has PTSD flashbacks to some missing days following the opening scene. He becomes certain that he's still being abducted (apparently by German soldiers), but Kate is worried about his seemingly paranoid behavior.

We also meet a woman named Sally Clarke, whose husband Fred is a travelling salesman, who often leaves her behind to look after their young children, Tom and Becky, by herself. While he's away, Sally finds a wounded man named John (Eric CLose) in her shed, and gives him shelter. He's actually the missing alien, as they can alter their appearance to look human. Eventually Sally and John make love, and John impregnates her. Soon after that, he leaves, to avoid Owen's men, who are closing in on him. Before he leaves, Sally gives him one of her star-shaped earrings.

Russell learns that the most of the men he served with, who also experienced missing time, have died mysteriously. He goes to visit the last surviving man in the hospital, and from him he learns more about their missing time. Sue brings the artifact she'd found to Owen, who later kills her and marries Col. Campbell's daughter, Anne, to advance his career. Campbell hates Owen, but Owen blackmails him into a promotion to major, and being put in charge of the colonel's project studying the recovered UFO. (I really don't like Campbell, but Owen is much worse; he strikes me as a sociopath.)

Episode Two: Jacob and Jesse
In 1953, Russell is gone, and Kate is remarried to Sheriff Bill Walker (Ian Tracey, whom I mainly know from Sweating Bullets). Kate and Russell's son, Jesse, gets abducted by aliens, in a rather cute CGI sequence where an alien takes the form of an anthropomorphic squirrel from a story Kate had been reading him at bedtime. But he's soon returned, and the story skips forward five years, to 1958. Owen (now a colonel, and father of sons Eric and Sam) is upset that his team has spent more than ten years studying the flying saucer without learning anything about it. So he brings on an aerospace engineeer named Dr. Kreutz (a former Nazi) to study it. Kreutz immediately gets the idea that the aliens used mental abilities to power the spacecraft, so Owen wants to find people with psychic powers to further their research of the craft.

Russell is a hobo now, hopping trains, but still being abducted by aliens, as is Jesse. At Christmas, he gets Jesse to run away with him. Bill and the police eventually find Russell, but Jesse has been abducted again, and Russell gets arrested. Meanwhile, Sally (who is now widowed) is obsessed with contacting John in outer space, so she's built a machine to do that. She takes it with her to a New Year's Eve convention of people who all believe they've had contact with aliens, many of whom have built similar devices. She has a son named Jacob (Anton Yelchin), who has psychic powers inherited from John. Tom and Becky are grown up now, and want to get Jacob to go away to a school for special children, though Sally wants him to stay with her. They are also concerned about their mother's belief in aliens.

Owen recognizes Sally in a photo from an earlier convention she attended with Jacob, and goes to the New Year's convention, and tells Sally some lies. He sabotages her truck so he can give her a ride home, secretly so that he can meet Jacob. But Jacob knows why he's really there. Owen abducts him, but he eventually escapes using his psychic power, and is found by Tom and Becky, who bring him home. Sally decides she wants Jacob to go to the school Tom and Becky had found for him, and fakes his death to keep the Army from looking for him (though after what he did to Owen's mind, Owen just wants to forget about him). Sally gives Jacob her star-shaped earring, which she has been wearing as a necklace since giving the other earring to John in episode 1. The aliens return Jesse, and Russell is released from jail, though Bill still blames him for Jesse's disappearance, and warns him never to return. Anne believes Owen was having an affair with Sally, and wants to leave him, but Owen won't let her, saying she knows too much about the top secret work he does.

Episode Three: High Hopes
In 1962, Jacob (whom everyone at the Greenspan School know as "Jack") learns that if he continues using his powers, it could kill him (or he could just lose his powers). Russell and Jesse learn that they have brain tumors that could kill them (or not). Owen is concerned that President Kennedy will shut down his project if he can't prove that aliens pose a clear and present danger. Bowen and Erickson come to hate Owen, who treats them as disposable. They decide to search for Jacob. They find him, but he gets away, using his power. He is helped by Dr. Ellen Greenspan, who delivers him to Tom and Becky, who take him to stay with someone else. Anne has become an alcoholic/drug addict. Jesse decides he and his father should find the people in Air Force who are in charge of the UFO project, and eventually he finds Owen. Things go very badly for both Russell and Jesse. Russell dies, and Jesse is arrested as a spy. Later, Owen kills Bowen and Anne. He frames it as an affair turned murder/suicide. Also the Cuban Missile Crisis happens. And aliens abduct Jesse agaiin.

Episode Four: Acid Tests
In 1970,