Christine was pushed into the anomaly at the research center by Helen and was killed by a Future Predator. Since then, the research center has been abandoned. Danny believes that Helen’s maniacal obsession with altering the past will not stop until she has destroyed the human race. He decides that they must stop her. The team assembles to follow her into the future using the anomaly at the racetrack testing site. At the same time the anomaly detector goes off at Christine’s research center. Danny sends Becker and Sarah to check out the new anomaly while he, Connor and Abby go into the future.
In the future the team is chased by Megopterans. They find an anomaly and trick the Megopterans into entering it. The anomaly turns out to be the one that Christine had originally cloaked at the research center. When Becker and Sarah get to the center, they end up battling the Megopterans.
Danny, Connor and Abby find themselves at ARC but in the future. They find Helen who is working with the artifact at a computer console. The team learns that Helen plans on going into the past and killing early man so that the human race cannot evolve. That way the Earth will be saved from the cataclysmic event that brought about the destruction of the planet. Helen destroys the artifact and escapes through an anomaly, using a handheld device, to the Cretaceous period. The team finds a way to follow her. In the Jurassic period Connor gets injured. Abby stays with Connor. Danny follows Helen into a new anomaly and ends up in Pliocene Africa. The oldest place where known hominids existed.
Episode 10 of season 3 features the return of Future Predators, Megopterans, Raptors and a Pteranodon, and introduces Austalopithecus (early man).
The Austalopithecus that Helen killed are based on a real fossils found at that same location (333 is in the Great Rift Valley in Africa). The reason for the deaths of the hominids is not known but it is suggested that they died in a flood.
The Future Computer was a device from the ruins of ARC in the future. With it you could locate every anomaly there ever was or ever could be. The computer was a large touch screen, with two sockets: one for insertion of the Artifact and the other for a handheld Anomaly Opening Device. Information was transferred from the Artifact through the computer onto the handheld device. With the Opening Device you could also select the time period you wanted for the anomaly created.
The third series ends in a cliffhanger with Connor and Sarah stuck in the Cretaceous period and Danny stuck in Pliocene Africa.