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.