The time is that of "almost tomorrow." The planet is in dire straits and the government is falling apart. With no alien activity for months, the Blackwood Project is lost to explain the situation.
To make matters worse, a new set of aliens, the Morthren, have arrived on Earth and have set out to accomplish where those before have failed.
What remains of what was once the Blackwood Project search out a new home, as the Morthren likewise look for a new base of operations.
While the Morthren use a cloned reverend to teach humans of the Eternal, the Blackwood team find a valuable piece of the Morthren's cloning process.
A heat wave strikes the city, but one church's sudden supply attracts people of the faith. Little do they know, however, that they are pawns of the Morthren in an attempt to sway human faith to that of the Eternal.
With their lives in danger due to random acts of violence on the street, agitated by the rock and roll band the Scavengers, the Morthren decide to take advantage of the situation. With the frontman cloned, the impressionable audience will now have their violent urges directed by the Morthren's will.
The Morthren use a hospital to experiment on humans in order to increase their numbers.
Harrison falls for Seft of Emun, a slave to the Morthren race, brought out of stasis to restore their power.
A defiant young Morthren boy named Ceeto runs away from the rule of his kind and makes friends with Debi.
Seeing the destructive effect the city life is having on Debi, Suzanne decides to take her daughter to her family farm. Little do they know, however, that the Morthren have taken the farm over to deal with their own food shortage.
The Morthren begin to take over a rehabilitation centre and treat patients with a new drug composed in part of human brain tissue.
An attempt by the Morthren to hack into a computer system backfires, scarring a technician. Now flawed in the eyes of the Eternal, he faces execution, but escapes and questions the ways of his people.
Under the Eternal's instructions, Malzor takes advantage of a rare opportunity to go back in time to 1953 in the aftermath of the failed invasion in order to prevent their brethren from succumbing to Earth's bacteria.
The Morthren use the first-born child on Earth, who has grown rapidly since birth, to infiltrate an experimental school and steal useful genetic information.
An illness strikes the Morthren and only a stolen med cell can cure them. The Morthren use a clone to seize it, unaware that a war is brewing on the market.
Nosey reporter Marc Traynor is caught in the middle when he has photographic evidence of both the Morthren, as well as the identities of Harrison and Kincaid.
Suzanne gets Kincaid and Harrison to help plot a surprise birthday party for Debi.
The Mothren clone a popular motivational speaker to use for their own sinister purposes.
Debi is snared into playing a deadly game that the Morthren have infiltrated.
A year after the death of Kincaid's brother, the Morthren resurrect Max as a killer cyborg.
With their situation becoming dire, the Morthren frame Harrison, Suzanne, and Kincaid for a bank robbery. The team's only hope lies in the department's one virtuous cop.
After consulting a sacred obelisk, Malzor orders the Morthren to use a deadly spore to wipe out all Earth-born life on the planet. However, the obelisk holds a secret that could end the war of the worlds once and for all.