After the destruction of theEspheni power core, the Espheni were left disorganized and without their mechanized servants. Taking advantage of this and at the behest of the Dornia, Tom Mason organized a Global Resistance against the Espheni to finish the job and kick them off the Earth. As part of this, Tom began organizing all the militias in the former United States for an attack on Washington, D.C. where a major Espheni base was. Eventually the 2nd Mass's efforts led them to discover the Espheni Shadow Plane device and Ben Mason was able to discover the existence of the previously-unknown Espheni Queen from it. The Dornia and the Alexisclone inform Tom that the queen only comes to a planet when victory is assured and that the queen's presence provides an opportunity to defeat the Espheni once and for all: the Dornia are able to provide Tom with a bioweapon that when used on the queen, will kill the entire Espheni race. While the weapon is initially harmful to humans as well, Anne Mason and Marty are able to modify it so that it only affects the Espheni. The weapon's effectiveness is proven when its used to kill the Alexis clone and they learn from a clue Ben discovers in the Shadow Plane that the queen is at the Lincoln Memorial. However, a Black Hornetattack on the 2nd Mass and 14th Virginia base delays their departure until the next day. Before they can leave, word is received that Washington, D.C. is surrounded by a powerful defensive wall that will be incredibly difficult to breach. As a result, instead of an all-out attack on the Lincoln Memorial as they had originally planned, Tom decides to have the other militias assault the wall as a distraction while he leads a strike team through Washington's service tunnels in a surgical assault to assassinate the Espheni queen.
Led by Lieutenant Demarcus Wolf who grew up in Washington, D.C. and played in the tunnels as a kid, Tom's strike team makes its way through the tunnels as the other militias assault the wall. The Mason militias face enormous resistance as they attempt to bring down the wall, resulting in a confrontation with Skitters, Black Hornets, Wapers, Skitterized Humans, and multiple Espheni Overlords. Meanwhile, the strike team discover Espheni eggs in the tunnels and try to avoid disturbing them as Cochise warns of how dangerous the hatchlings are. However, a curious member of the team disturbs one and the hatchlings awaken, killing him. As the team desperately tries to fight the hatchlings off, Wolf uses a grenade launcher to blow them up. However, Wolf is buried by debris and killed while Anne Mason is mortally wounded by shrapnel from the explosion. Tom Mason is left uninjured, but is separated from the rest of the team and continues on alone while the team tries to find another way out of the tunnels. Tom eventually emerges from the tunnels near the Lincoln Memorial and spots the battle occurring between the Espheni and the militias attacking the wall. He realizes that the Espheni are settling in on Earth and moves into the ruins of the Lincoln Memorial where he comes face to face with the Espheni Queen. The queen pins Tom to the wall with webbing, causing him to drop the Dorniabioweapon before he can use it on her. The queen explains how the Espheni had tried to invade the Earth 1,500 years ago and failed. As her beloved daughter died in that invasion, the queen wanted revenge, the true reason behind the Invasion of Earth. After showing him the past, the queen begins to drain Tom's blood from his body. Tom manages to reach the Dornia weapon and infect himself with the virus as the queen drains his blood. Due to Anne and Marty's modifications to the weapon, Tom is immune to the virus' effects, but the virus passes into the queen through the blood she drains from him. Despite the queen quickly pulling her sucker from Tom and stopping the blood draining, its too late and the virus quickly takes effect, killing the Espheni Queen and causing her to explode into ash. As a result of the queen being biologically connected to her entire race, the Dornia virus passes from the queen into the rest of the race, causing the Espheni all over the planet to explode into ash. The virus does its work and the Espheni are wiped out.
With the extinction of the Espheni, the Invasion of Earth ends and the Earth is finally freed from Espheni control. Tom Mason discovers that his wife died of her wounds and desperately takes her to the Dornia in hopes that they will save her since he got them their vengeance when he wiped out the Espheni. The Dornia resurrect Anne and humanity starts to unite in the aftermath of the invasion. Months later, thousands of people and some Volm gather at the Lincoln Memorial to elect a new leader for the human race and listen to a speech by Tom about how humanity now has a second chance as a united race.