Shortly after her ship's capture by the Resistance, Diana escapes in a shuttle but is pursued by Donovan. The two engage in combat in the atmosphere, and Donovan successfully shoots her down and, after a short fight, captures her.
One year after the day when the Red Dust was deployed, now the international holiday called "Liberation Day", the former members of the Resistance and their Fifth Column allies have gone their separate ways and are each looking forward to prosperous careers and bright futures. When Diana is finally put on trial for the atrocities she committed during the First Invasion, Science Frontiers, the company responsible for mass production of the Red Dust, at the behest of its CEO Nathan Bates, arranged for Ham Tyler and his security firm to publicly "assassinate" Diana on her way to the trial and take her to a secret cabin in the woods outside L.A. After this is done, Nathan offers Diana better accommodations in exchange for helping to solving problems such as disease and environmental failure on Earth by providing Visitor technological information.
Donovan and Martin, having witnessed her supposed assassination, sense something isn't right and pursue Tyler's agents in a stolen helicopter. After reaching the cabin, Donovan is knocked unconscious by Martin, who wants Diana dead. Before Martin can kill her, Diana is able to overpower him and steal his pistol. She forces him to surrender his last antidote pill so she can temporarily survive on Earth and then shoots him, effecting her escape to the Southwest Tracking Station.
Martin tells Donovan about Diana's plan to make the Visitor Fleet return moments before his death, and Donovan sets off on foot. Donovan meets Tyler and agree to pursue Diana together. Attempts to stop her fail, and Diana escapes to a Visitor Shuttle arrived from a new fleet hidden behind the Moon, and Diana proceeds to launch the Second Invasion of the Earth.
The Resistance assembles once more, now fighting the Visitors nationwide and also contending with the power-hungry Nathan who has used the power vacuum of the collapse of the government and authorities to become Governor of Los Angeles. The Resistance fights however it can, often joined by other rebel groups, but cannot use their Red Dust super weapon, due to toxic long-term effects it will have on the Earth. Meanwhile, Elizabeth, who has transformed yet again and is now looking 18-years-old, becomes increasingly important in the cause for Earth's freedom and eventually leads her to control the destiny of either race and decide the outcome of the conflict