March 3, 1946: Maia Rutledge, an eight year old blonde girl is at a picnic with her parents in California. Since it's raining they are waiting for it to subside in their car. Bored, she asks them to let her wander the surrounding area. As she picks up some flowers, a bright light appears over her, then vanishes with her.
May 11, 1951: Richard Tyler, a colored Air Force pilot, is being beaten up by several white soldiers during the Korean War. One of the soldiers advises him to put in for a transfer. As he contemplates a picture of him and a blonde woman, the same bright light that appeared over the young child five years ago disappears with him in the same fashion.
June 11, 1979: Orson Bailey, president and partner of an insurance firm (Kensington and Bailey) in Tacoma, is ready to celebrate his 35th wedding anniversary in a nice restaurant with his wife. While Orson is getting ready to pick up his wife, the light appears over him as well.
April 22, 2001: Shawn and his cousin Kyle are hanging out, drinking a few beers and talking about Nikki, Shawn's 14-year-old neighbor. A bright light appears over them and as it approaches them, Kyle falls unconscious and is left in a coma for three years, with Shawn missing since that day.
Present Day: Tom Baldwin visits his son Kyle in the hospital every day, obsessed with finding his nephew Shawn, in the hopes that he can explain what happened to Kyle. Local residents are excited about a comet passing by, but its trajectory changes to a collision course with Earth, sparking a panic. The Seattle Branch of the Department of Homeland Security monitors the path of the comet very closely. Soon after, China, USA, England, France and Russia all launch missiles at it with no affect whatsoever. Diana Skouris, one of the federal agents, is led to believe that it might not be a comet at all. The team tracks the "comet" which has decreased in speed, to Mount Rainer. The "comet," which actually turns out to be a bright mass of light, disperses in a concussive burst. As the fog from the blast clears out, thousands of people can be seen, as if they just appeared out of nowhere. Among them, are men, women and children – including Maia, Richard, Orson and Shawn – of all ages and nationalities. Tom is watching at hospital and after seeing Shawn among the returnees he goes to see his boss, Dennis Ryland, to ask for his old job back. Ryland decides to team Tom with Diana, to the dismay of the two agents.
Meanwhile the returnees, currently being held in quarantine, begin to grow restless. Still in quarantine, Tom goes to ask Shawn about what happened to Kyle and mistakenly implies that it was Shawn's fault. Shawn's concern for Kyle turns in to anger towards Tom, and he storms out. Richard and Lily, another returnee, share a short conversation in which he mentions Lily looks like someone he used to know. They discover that the blonde woman in Richard's picture was actually Lily Bonham, Lily's grandmother. While Orson speaks to a representative in quarantine about making a phone call, Maia walks up and gives Orson a handkerchief just seconds before he has a nose bleed. Later, they are seen watching a screen in which Barbara Yates (a popular TV talk show host) is criticizing the returnees. Maia states that she doesn't like them much, and he retorts that the feeling is mutual. After a series of preliminary interviews and medical exams, the returnees are released due to the lack of a legal right to hold them.
After being released, Lily goes in search of her family (who didn't show up to meet her at the center) while Richard heads to St. Louis. Excited, Lily returns to her house, but is told by her (now) ex-husband Brian that he is re-married and their daughter Heidi knows nothing about Lily. Lily insists on seeing Heidi, causing Brian to issue a temporary restraining order to keep her away from Heidi. While at a celebration for his return, Shawn is outside talking with Tom when a bird flies in to the window. Shawn picks it up, stating it's neck is broken; seconds later it flies away, uninjured. Tom is perplexed. Later, Shawn gets into a fight with a guy at school and manages to pin him to the ground. He seemingly drains the life out of him, but ceases just before killing him. Maia gets adopted, and during her first night at her new home she tells her foster parents she doesn't want her shoes on the floor because they'll get wet. Meanwhile, Richard is having little luck as well. His old home is gone, and with his relatives dead he has nowhere to go. He decides to return to Seattle to find Lily. Back at Maia's new home, the washing machine's water hose breaks, flooding the nearby rooms (including the spot where her shoes were). The next day she goes to visit her parents' grave, accompanied by her new parents. They quietly discuss how run-down the area has become, and get scared when Maia tells them they'll be buried in the nicer cemetery down the road. The following day they get a brochure from the cemetery she had mentioned. They later decide to bring her back to Homeland Security, assuring her it's not her fault.
Orson Bailey manifests a power as well. When he gets angry, his nose bleeds. After going to see his wife in a nursing home Orson visits his former firm, intent on getting his job back. However, his partner's son is currently running the company and informs him that his interest in the firm was bought out, with no available openings right now. Later that evening, upset that his wife is in a degrading nursing home, Orson visits Eric Kensington and unwillingly causes some sort of tremor. The glass from the windows and doors in Kensington's house shatter, and Eric dies of massive skull fractures. Orson is subsequently arrested, but without evidence are forced to release him. Tom and Diana question him, witnessing Orson's power when they pressure him. Orson goes to visit his wife and is told that she passed away, which makes him to cause another tremor. He disappears, prompting Tom and Diana to track him down. Lily and Richard meet at the park she used to bring Heidi to before her disappearance. They discuss how both of them have nowhere left to go, and decide to start looking at an apartment together. They question whether or not they were meant to meet each other through the will of their captors.
While at a doctor's office for a checkup, Lily is told her nausea isn't because she's sick; she is pregnant. The two become even more curious. While looking at an apartment later that day Lily suddenly becomes uneasy, as if the baby is telling her she doesn't like the place. They later settle on a different apartment. Tom and Diana manage to locate and confront Orson at an isolated lake cabin, where Diana is forced to shoot Orson (non-fatally). They return him to the quarantine facility. While discussing the incidents involving Orson, Diana asks Tom if he noticed anything similar about Shawn, and he hides the bird incident from her. Shortly thereafter, Shawn visits Kyle in the hospital. As he puts his hand on Kyle's chest, Kyle awakes and sits up for a second, then falls back, still comatose. Shawn backs away stunned at the episodes close.