In 1961 fresh-faced idealist John Loengard and girlfriend Kimberley Sayers arrive in Washington DC and uncover evidence of a plot to keep secret the existence of aliens.
Following the Kennedy assassination, Bach heads for Dallas to recover the artifact Loengard used to prove the alien invasion to the President. However, Robert Kennedy sends Loengard to recover it. John meets Jesse Marcel, a government official who claims that the alien craft suspected to have crashed there was really shot down. He leaves Marcel to follow Majestic's Jim Steele to a Dallas nightclub, where he and Kim discover that Steele is really a Hive spy arranging for club owner Ruby to kill Lee Harvey Oswald. John looks for an Air Force pilot that Steele spoke to in Dallas and finds that a military fly-over scheduled for the President's funeral is really a suicide mission to kill the assembled world leaders.
A dream draws Kim to Florida. Because Bach isn't far behind, John only reluctanly agrees to help find the astronaut she's seeing. As Majestic prepares a secret space probe to locate the alien base, Kim and John arrive in Cape Canaveral where she spots Ty Yount, an astronaut who was with her on the alien ship: it turns out not all the unmanned NASA missions were unmanned. Although suspicious of anyone connected with Majestic, Yount reveals that he's being sent on a secret space mission to combat the invading aliens. Sure that she and Yount were aboard the alien ship at the same time, Kim agrees to undergo hypnosis, and remembers Yount being deemed unfit by the aliens and discarded. Another dream helps Kim remember seeing another astronaut implanted by the Hive. With Yount and his partner scheduled for another secret mission, John and Kim warn Majestic that one of NASA's crew members is part of the Hive.
John and Kim uncover a Hive plot to use the Beatles' American television debut to induce mass suicide amongst the 'throwbacks' -- the abductees who were not implanted.
While probing a Hive operation in Las Vegas, John and Kim encounter eccentiric casino owner Howard Hughes. Hughes thinks the Hive are communists. Hive members are using their telepathic abilities to win at the casinos and using the money to dig a tunnel near a secret military installation. Kim still has enough of the Hive in her to 'hear' them.
A series of strange sightings and unexplained deaths at a dairy farm lead John and Kim to suspect the Hive are using livestock in their plans.
John and Kim uncover the connection between the 1964 Alaskan earthquake and an ancient legend.
John and Jesse probe a UFO sighting: could this be the evidence they need, or is Majestic using them for its own ends? Kim goes to her sister's wedding, discovers evidence that her sister's fiancé is a Majestic agent, and is stalked by Steele.
John and Kim find a Hive operation in Meridian, Mississippi, where three civil rights workers are missing and feared dead. A white supremasist has been impregnated by a ganglion, but resists full takeover, because other Hive hosts are black.
John and Kim travel back to LA to investigate the suspicious suicide of an old friend. They encounter a young film student, Jim Morrison, who helps them stop the Hive breeding and distributing a bacterium.
John's brother Ray is becoming part of the Hive. But when their father refuses to believe the invasion, John finds himself committed to a psychiatric hospital.
Bobby Kennedy persuades John to talk to the Warren Commission, which is looking into the assassination of JFK. But Bach is determined to discredit him.
Bach's pursuit of the wreckage of an alien ship helps bring about American involvement in the Vietnam war. Kim and Juliet, the Russian observer, involve Bach's wife to get John back.
John and Kim use an alien glyph decoder to draw an alien Gray ship into a Majestic trap. They miss the ship, but capture a Gray. And once its Hive implant is removed, it can communicate with Kim.
Kim feels compelled to have her baby in California, but is the compulsion from Majestic, or from the Hive? And she arrives just as race riots break out in the Watts area of Los Angeles. The Gray finally wakes up, but too late to save Kim from being captured by the Hive.
Steele tries to persuade Kim, her ganglion regrown, to return to the Hive willingly, telling her it's the only way she can be with her baby. He's also trying to fuel an anti Vietnam War riot, because Majestic's funding is linked to war funding.
John and Juliet travel to New York to stop a stolen film of the aliens being shown on the news. The Hive, in the shape of Steele and Kim (who feels nothing for the baby she is reunited with), are also after the film.
Juliet, John and Major Colin Powell investigate an attack at their Soviet counterpart's HQ. Dr Carl Sagan is enlisted to help find the Greys' home planet.
It's the Summer of Love, and the Hive are distributing 'brown cubes', drugs that put you in contact with the Hive mind. Steele takes on the persona of Charles Manson; John gets a bad trip from Kim, and sees his son on the Hive ship. Carl Sagan decodes a Grey message, warning that the main ship will arrive at the Millennium, and also works out how to predict abductions of various 'bloodlines'. The next abduction will be Ronald Reagan. So John offers to take his place, to infiltrate the Hive's mother ship, gain critical data, and find his son. Meanwhile, Albano has gone over to the Hive, and wrests control of Majestic from Bach.