Following a message from his congressional colleague Mark Simonson, John and Kim are drawn to Meridian, Mississippi, where the struggle for voting rights is clouded by the disappearance of three civil rights workers. As Kim senses the Hive's presence in the town, news that Loengard is in Mississippi prompts Bach to act. Then, after being contacted by Etta Mae Tillman, John and Kim are led to where Simonson is hiding after escaping the deadly fate of his three missing civil rights co-workers.

Following the suspicious suicide of college classmate Robert Dewey, John and Kim arrive in Los Angeles to see their old friends Nat Heller and Gina Abbott. Learning that Dewey's corpse was mysteriously confiscated by someone claiming to be with the coroner's office, Kim heads to the funeral home to investigate. Upon discovering a cameraman lurking in the bushes, she meets film student Jim Morrison, who has documented the removal of Dewey's body. And though John is suspicious, Kim befriends Morrison to find out just what he knows.

Following the deaths of both President Kennedy and his assassin, Bach realizes that the alien hive has planted a spy inside Majestic - and all the evidence points to his trusted aide, Jim Steele. However, Steele escapes into the Majestic complex after a failed attempt to eject the alien ganglion from his body. Meanwhile, Loengard and Sayers return to John's childhood home in California, where an uneasy reception from John's older brother Ray revives long-standing tensions between them.

With the Warren Commission looking into the assassination of his brother, Attorney General Robert F. Kennedy asks John to testify. Despite Bach's warning, Kennedy paves the way with his own testimony before Loengard describes the events that led him into Majestic. And while John has a long way to go before convincing a skeptical Supreme Court Chief Justice Earl Warren and his fellow commission members of his story, Bach decides to thoroughly discredit him anyway.

When Soviet operatives fire on a Hive ship over the Gulf of Tonkin, Bach claims that US naval vessels were their target and starts the country's involvement in the Vietnam War. After air strikes down a Hive ship, Bach kidnaps Loengard for a reconnaissance mission. Yet, when military officials express reservations about having Majestic's Juliet Stuart co-ordinating with Russians also tracking the Hive, Bach joins Loengard for the trip himself. Teamed with Vietnamese guide Tay Ma, Loengard comes across a crazed American soldier as he finds a Gray's severed head. And when John finds that the crash site has been visited by the Viet Cong, Bach orders him to destroy it while requesting an air strike that could kill them all.

Despite tensions between Loengard and Albano, Bach is determined to get a glyph decoder held by Juliet. Realizing that it's just the weapon that could help with a takeover of Majestic, Juliet agrees to let Bach use it to attract an alien ship. As Loengard, Sayers and Juliet work to replicate the crop circles suspected to denote landing sites, the young daughter of a widowed farmer slips into where they are working. And upon taking her home, John and Kim can only hope Monica Gresham hasn't seen too much. Then, as their ruse succeeds in attracting a ship, an attempt to capture it and the crew goes awry. So Bach gives John and Kim time to find a wounded Gray on their own. Seeking refuge at her father's farm, the alien enlists Monica's help by promising her a chance to see her dead mother. Sensing that the Gray is nearby, Kim and John set up surveillance. Finding Monica looking for another critical artifact left behind by the ship, they follow her home to where the Gray is hiding. And thou

When Kim feels strangely compelled to have her baby in California, Bach sends her to a doctor working with pregnant mothers who were at one time abducted by the Hive. As Kim arrives on the West Coast where she will be observed along with expectant mother Ruby Thomas, race riots have broken in Watts. Then, as Loengard befriends fellow father-to-be George Thomas, the Gray being kept under observation at Majestic emerges from its coma as Kim and her unborn son are kidnapped in L.A. by the Hive. And using one of Majestic's alien artifacts to communicate with Gray, Albano learns that it feels betrayed by Kim.

As Steele works on Sayers to willingly accept returning to the Hive, Loengard seeks anyone he believes can lead him to his wife. So, when Bach Juliet to Berkeley where the Hive is infiltrating the growing antiwar movement, John insists that he go along, to, unaware that he's being used to locate Kim. Although John spots her, he is unable to stop Kim from Joining Steele on a trip to visit her son. And as John and Juliet question antiwar activist Jerry Rubin about here whereabouts, back in Washington Bach sees that the Vietnam War can be used to increase funding for Majestic.

When film of Truman's meeting with the aliens is stolen, Bach sends Loengard to see Carl Hertzog, a retired Majestic doctor. After denying any knowledge of its whereabouts, Hertzog is hanged to death in what appears to be suicide. Then, as Albano discovers the film in the hands of TV personality Dorothy Kilgallen, Kim learns that her child is destined for greatness with the Hive. Once Loengard and Juliet track her down to New York, Kilgallen asks reporter Ed Hawkins to air the film if anything should happen to her. And when Kilgallen refuses to heed Loengard's warnings, Albano's surveillance of her apartment spots Steele trying to recover the film. But before anyone can get there, she is killed. Meanwhile, as Kim infiltrates CBS as an assistant to their network news anchorman, Albano turns to network president and Majestic board member William Paley for help.

Following a disturbing message from the Soviet Union's counterpart to Majestic, Bach assembles a team that includes Loengard, Juliet and Army Major Colin Powell to investigate. While the team discovers most of Aura-Z's personnel are dead, they find a pair of researchers who survived. As Ludmilla and Pavel tell of experiments with prisoners that backfired and of the convicts who are now holding the head of Aura-Z and Juliet's mentor, Colonel Dmitri Mironov, back in the US, Bach enlists astronomer Carl Sagan in an effort to find the Hive's home planet.

Alerted to a planet size object transmitting a message to Earth, Bach orders Dr Carl Sagan to decode it while he keeps the news from Majestic's directors. And though he's kept in the dark, Albano agrees to ask the captured Gray to shed some light on its contents. Meanwhile, Loengard and Juliet use Dr Timothy Leary to find the San Francisco lab where the Hive has been producing a hallucinogen under the direction of Steele and Kim. And when Kim tosses the drug into John's face, it causes him to see their son aboard a Hive ship.