A new, more advanced generation of aliens known as the Morthren arrive on Earth. Dr Blackwood is saved from a kidnapping by a renegade soldier called John Kincaid. After executing the original alien invaders for failing to conquer humanity, the Morthren aim to destroy Blackwood's team with a clone of Colonel Ironhorse.
The remaining members of the team set up a new home and try to deal with their grief. The Morthren also have to find a fresh refuge and as part of this they kidnap and duplicate a priest who runs a homeless shelter.
The aliens take over the members of a punk rock band and add a secret electronic signal to their music which will drive young people into a violent frenzy. Meanwhile Kincaid begins a romance with his late brother's girlfriend.
When an alien weapon intended to kill humans via computer systems backfires, its creator, Kemo, is maimed in the process and then sentenced to death for his incompetence. Having developed human emotions as a result of his accident, Kemo teams with Kincaid to destroy the weapon.
The Morthren have developed a time machine. Malzor travels back to 1953 to inject his invading predecessors with an immunity drug to Earth's bacteria so they'll complete their original mission of obliterating mankind and colonizing the planet. Blackwood and Kinkaid arrive at the alien's research facility and follow Malzor into the past to try and stop him.
The alien embryo created on the "Breeding Ground"episode has now grown and is now a pre-adolescent in human terms (named "Adam"), residing in a special school occupied by human children with exceptional IQ's, secretly run by the Morthren. The aliens have nefarious plans for the children.
A revolutionary "med cell" is created that could save countless lives. But fearing that the Morthrens could turn it into something deadly, the Blackwood team tries to get their hands on it first. Meanwhile, Malzor desperately tries to acquire it to heal a dying Mana, his second-in-command.
In the midst of the post apocalyptic future, the team decide to throw a birthday party for Debi. Meanwhile, the Morrhren attempt to locate their malfunctioning "seeing-eye" device (a self-controlled drone), which has run amok through the city.
Kinkaid's brother Max had disappeared during their last mission prior to Kinkaid running into the Blackwood team. Now, the team stumbles across an imprisoned Max while infiltrating an alien stronghold and rescue him. Unknown to the team, Max has been transformed into a Robocop-like entity programmed to execute Kinkaid.
The Morthren have finally learned the identities of the Blackwood team. They use it to their advantage by creating doubles, framing them for an armed bank robbery where several people were shot dead. Malzor impersonates a city police officer and joins in the manhunt.