Still being pursued by the military and by Mary Crawford, Lisa makes contact with her Uncle Tom who suggest they go to his mother's house in Texas and eventually onto Mexico and South America. The fact that Allie can be tracked presents a major difficulty. Mary Crawford and Dr. Chet Wakeman have a serious difference of opinion on what to do about Allie, leading Mary to take some drastic action. As the military moves in, Allie has a fateful choice to make.

With Mary Crawford now aboard the disabled alien vessel, the military start to move in. She sees her grandfather and has a conversation with him while an army Lieutenant gets to talk with his late mother. In order to save herself and those she cares about, Allie uses her powers in a very special way. On the road again, Lisa, Charlie and Allie have to keep a low profile as their photos are constantly on the news. Lisa meets a relative she has never met before and Allie has to use her powers to save him.

With Allie Keys in government custody, the plan is to use her as bait to attract one of the alien vessels. Mary Crawford finds herself out of the project however when it's taken over by General Beers. Charlie and Lisa are desperate to find Allie and Lisa undergoes hypnosis to see if she can make a psychic connection. She determines that Allie is in North Dakota and they set off to find her. Mary Crawford, using her many contacts, gets the same information and they all converge on the US Army site. When the alien craft arrives, Mary takes drastic action.

Mary Crawford has joined her father's project but is proving to be cut from the same cloth as her grandfather as she is quite vicious and will stop at nothing to succeed. The scientists believe they have found a way to block signals from the implant. Charlie and Lisa meet quite by accident in a group therapy session and after subsequently undergoing hypnotherapy, realize that Charlie is the father of Lisa's 9-year old daughter Allie. When an emotionally unstable member of the therapy group shoots Charlie and takes all of the others hostage, Allie demonstrates remarkable powers. In order to save everyone however, Allie agrees to go with Mary Crawford.

Jacob Clarke dies at a relatively young age. His wife eventually re-marries but his daughter Lisa, five years after his death, is abducted by aliens. Eric Crawford is out of a job and back to civilian life after the aliens recover all of the artifacts from the Roswell crash. As the years go by the various characters go about their lives but in 1991, Crawford is called back to service when the payload aboard a spacecraft vanishes. Jesse Keys' son Charlie is a successful schoolteacher but has decided that he will resist any further attempts at abducting him. Lisa meets Charlie when they are both abducted; she finds out soon after that she is pregnant. Crawford tells his now adult daughter Mary about the work he has been doing and invites her to join him.

It's 1980 and Eric Crawford is now the head of the UFO program. Soon after his father's death, he blackmailed government officials into giving him the post. Jesse Keys is married but is becoming increasingly paranoid over his abductions and agrees to seek professional help. He soon finds himself under the control of the military. Jacob is married and still has his special powers. He returns to Texas and reunites with his family at their mother's death bed. He tells his brother Tom about his origins and Tom goes from being the biggest pessimist to the strongest believer in aliens. This catches Eric's eye who cannot help but wonder what made him change his mind. To get that information, he starts an affair with Jacob's sister Becky.

It's now 1970 and Colonel Crawford is forced to retire after claiming to have found a potential landing strip for alien ships, which turn out to be human-made crop circles made by Tom Clarke specifically to discredit him. One of Crawford's sons, Sam, sees a newspaper report of an archaeological find in Alaska that bears the same hieroglyphs as is on the metal object he keeps locked away. He travels to Alaska to see what he can find out. Jesse Keys is now a young adult but keeps a low profile traveling from town to town. He's also a drug addict but while recovering in a VA hospital he falls in love with a nurse.

Jesse Keys seeks out his father Russell and together they decide to report their abductions to the Air Force. Medical tests reveal that they each have an identical brain implant. Eventually they are directed to Colonel Crawford but the attempt to remove the implant from Russell's brain doesn't go as planned. At home, Crawford has to deal with his wife's increasingly erratic behavior. Crawford's men discover that Jacob Clarke is still alive in Montana and try to take him but they underestimate his powers.

It's now 1958 and Russell Keys has long ago left his family. During one of his abductions however, he see his now teenage son Jesse has also been abducted. Keys has been trying to find a pattern to his abductions in the hope of avoiding being taken. So he returns to his home in Illinois and convinces his son to run away with him. His wife, who is re-married to a police officer, is frantic particularly when Russell returns but Jesse does not. Owen Crawford is now a Lieutenant Colonel and in charge of the program resulting from the Roswell crash. Very little has been accomplished in the last 10 years so he fires the entire team and decides on a new tack. In Texas, Sally Clarke's son Jacob is now 10 years old and clearly has special powers. His half-brother and sister want to send him away to a boarding school to protect him but Sally is completely against the idea. She reconsiders after getting an unexpected visit from Crawford who tries to dupe her.

During a bombing mission over Germany in December 1944, Capt. Russell Keys apparently survives his plane crashing after seeing bright lights in the sky. After the war, he is plagued by nightmares where he is mistreated by strange beings. As the nightmares continue, he learns that 8 of his 9 crew members are now dead. In Roswell, N.M. in 1947, U.S. Army Captain Owen Crawford goes up against Col. Thomas Campbell who is hiding the fact that a flying saucer has crashed in the area. Crawford is determined to take over the project and sets about to undermine the Colonel's authority. He also learns that the aliens may appear in human form. In Texas, lonely housewife Sally Clark helps an itinerant, John, who she finds hiding in her shed. John moves on but Sally soon finds herself pregnant and is visited by Capt. Crawford.

Prince visits the Lexx warning of "Earth's date with destiny". Emotions abound as Kai begins to feel again and the Lexx's health is ailing. The alien mother ship reaches Earth.

A huge alien asteroid mothership plummets to Earth and crashes into the Pacific ocean, causing a great disturbance off the coast of Japan. Inside, Lyekka prepares to devour "Japaneseland." Kai and Xev take a moth down to Earth to retrieve Vlad's cryopod control unit, which will replace the broken one on the Lexx. Fearing that Lyekka will consume the entire universe if she is not stopped, Xev and Kai decide they must take action to stop her.

As the Lexx flies away from Earth toward a new planet, the crew discovers a strange organic bulb on the galley counter. The bulb opens and reveals two round berries and a small potted plant. A holographic image of Lyekka's face appears and informs the crew that this is her thank-you gift for their helping her on Earth. Lyekka tells Kai the potted plant - a Yowraa-Taang - will open and bloom if he sings to it. Stan and Xev have been given the berries, which Lyekka says are the rarest and most exquisite delicacy in the two universes.

Kai, Xev and Stan stop off in Las Vegas as they wait for a space shuttle that Priest is arranging for them. Without a moth, the shuttle is their only means of returning to the Lexx. They check in at the King Tut, an Egyptian-themed hotel that is run by a group of mobsters. In the hotel room, Stan sees an ad for Slave Girls from the 18th Dynasty on the television and decides to order "room service" for himself. Xev discovers a female wrestling cage match is taking place on the premises and decides to enter, not realizing that it is fixed so that the casino can extort money.

An asteroid mothership appears out of the blackness of space. A metal hatch opens and a tadpole-like creature shoots out and heads for the Lexx. Stan awakens from a nightmare in which he was eaten by Lyekka and discovers that the alien mothership is hovering outside of the Lexx. Before he can finish telling Xev and Kai what he has discovered, an alien who has assumed the physical appearance of Lyekka from Stan's dream appears on the Lexx.

The Lexx crew encounter a space capsule filled with a bunch of politically motivated twenty-year-olds (Haley, Amber, Ryan, Josh). They claim that they have gone up in space with the intention of transmitting a message to make a political statement about the dying earth, and globalization. With financing from Haley's trust fund, they were able to pay the Russians to help them get up in space.

About to be destroyed, Prince requests Kai complete their game of chess, but this time with real stakes. Should the undead assassin win, he'll get his life-essence back. Should he lose, Stan and Xev's lives are forfeit.

As the Lexx's hunger becomes critical, it starts to slowly digest itself. Hoping for an alternative way off the Earth, Xev contacts Doctor Longbore, getting permission to join him on the space ship. This does however leave the Lexx wide open for Prince, who orders the President and Bunny to take a shuttle up there and take control of the ship using the key.

While the president finds himself haunted by Prince in the form of a TV set, Stan, Xev and Kai are abducted by Field Commander Moss, leader of the American Freedom Rangers, a para-military group devoted to freeing the American people from the grip of the Beast - Isembard Prince.

Wanted for murder, and the whole area swarming with police and FBI, Stan, Xev and Kai seek refuge in "Mort's Funeral Parlor". Mort takes an unusual interest in Kai's protoblood, hoping it can bring back to life his one true love.

Without the key the Lexx can't do anything, so Stan and Xev decide to settle on Earth. They pick the quiet country town of "Prime Ridge", but soon manage to stir up trouble.

In order to get a lead on the whereabouts of the key, Prince goes along with a rather twisted plan cooked up by 790.

As the alien carrot probes start to infest more and more of the planet, Prince sees his best option to escape up to the Lexx. Unfortunately, one of the killer vegetables follows him up there.

Kai and Stanley seek out the "Feast of Mograth", hoping to resurrect Xev. There they meet Oberon, king of the faeries, who grants their request... But in return demands their eternal servitude unless they can escape his forest before sunrise.

Trying to get back on the Lexx, Stan, Xev and Kai run across two druids who recognize them as holy figures. Promising to accompany the druids to a religious ceremony, Stan and the others are transported to the space shuttle. They steal it and find their way back to the Lexx thanks to 790, however unbeknownst to them, Vlad is waiting for them aboard...