Nufai is appointed commander and they begin to use the Purifier to destroy the Earth. But Kamal Re'x appears with a massive force of troops, and Orlok almost defeats him, but Nufai shows up and helps Kamal destroy Orlok, revealing that he was working for Kamal the entire time. The prince and his forces join Orlok as he tries to capture a communication center to contact the others who want to separate from the Hierarchy. He tells Orlok that he would be happy to overthrow Kamal's regime, so Nufai is sent to secure the Purifier while Orlok tries to make an alliance with the Masari queen, but instead finds her son, Prince Zessus. Nufai, a spy working for Kamal, used to be part of a species that the Hierarchy has since eliminated. Orlok, who has been questioning Kamal's intentions prepares to separate with others who follow him. Though the Masari mothership initially creates a signal that prevents the Purifier from being used, the Hierarchy bombard the ship from orbit and Orlok boards it to destroy the jamming signal transmitters. With the Novus portal destroyed and their forces scattered Kamal gives the order for the Purifier to be primed for activation, however, while distracting the Novus from the Purifier, Hierarchy field commander Orlok accidentally trips an ancient alarm in the Egyptian pyramids, and the Masari, asleep beneath the Earth's oceans, begin to waken. She manages to escape from the crashing ship but is unable to warn the Novus forces before they launch an attack on the Novus command base, damaging the portal that Novus were planning to use to return to Earth and forcing the Novus leader, known only as the Founder, to sacrifice himself to prevent it from exploding and destroying what's left of the Novus forces. Over the course of these missions the Novus field commander Mirabel, a cloned member of Novus' creator species, manages to befriend the human General Moore, in charge of leading what's left of the US forces after the initial Hierarchy invasion, and together they are able to launch an attack on a Hierarchy Material Conduit and use it to enable Mirabel to board one of their command ships, learning that Kamal Re'x, the overseer in charge of the Hierarchy forces on Earth has purposefully delayed the Purifier's activation in order to use it to destroy the Novus forces when they arrive on Earth before scuttling the command ship to kill Mirabel.

They then proceed to establish bases, using guerrilla tactics to harass the Hierarchy while investigating why the Hierarchy has delayed in using their ultimate weapon 'the Purifier', to utterly eradicate all life on Earth and proceed to strip mine the planet. The Novus (a race of machines who fight the Hierarchy to avenge their fallen creators) arrive just in time to save Washington, D.C. Because the Hierarchy has vast military experience from invading and destroying other planets in the universe, the human race is not able to withstand their forces.

Before their landing, observatories and scientists on Earth gave warning of aliens but the human race, as a whole, is not able to organize a unified military front against the alien forces. Universe at War: Earth Assault, begins in the year 2012 when an alien race known as the Hierarchy lands on Earth to strip-mine the planet.

Universe at war hierarchy