Tom Mason, a history professor from Boston who almost always wears the same bike gloves, is made second-in-command of the 2nd Massachusetts Militia Regiment, a group of civilians and fighters fleeing the city.

Meanwhile, Terry Clayton (Henry Czerny), an old friend of Weaver's and the commander of another survivor group, is revealed to be a collaborator who is giving human children to the Skitters.

When Skitter forces draw back in major cities, the 2nd Mass decide to launch an offensive on the alien base in Boston; Tom and Weaver scout it to detect weaknesses.

When given the option of joining forces with the approaching Skitter rebellion, Manchester refuses and eventually orders that all members of the 2nd Mass be arrested.

Also, the human resistance and their Skitter allies have formed an alliance with the new aliens, known as the Volm, who have provided them with the technology to effectively combat the Overlords, whose name has been revealed as being the Espheni.

While Tom carries on his duties as President of the New United States, he has to deal with many of the hardships of being a leader - including the issue of a mole within Charleston.

Anne later gives birth to Tom's daughter Alexis, but his joy is short-lived when Charleston is attacked by a group of soldiers working for a man they call the President of the United States, Benjamin Hathaway.

Then, with the help of Lt. Fisher, Tom makes contact with Benjamin Hathaway forces and decides to travel to Keystone to meet them along with Cochise, Pope and Bressler.

When Tom has recovered enough to walk around and resume his duties, he is thrust into further danger when his son Hal, implanted with an Espheni eyebug, attacks him and Peralta as they are discussing the Volm weapon.

To his horror, he finds himself abducted by Hal, who demands information on the Volm weapon, and ends up being held hostage in a nearby building which the 2nd Mass later surrounds.

Tom later decides to return to the Pickett house to check on their well being, after telling them about Charleston, but is ambushed by several Espheni mechs and skitters.

Now captured by Karen, Tom awakens in a dream world where the invasion has not happened and he and his wife and sons have been living a normal but happy life.

After initially trying to attack Karen, Tom breaks down in tears and is then shown the activation of the Espheni planetary defense grid and is informed that within three months all life on Earth will be lost.

When another explosion rocks Charleston, killing many and wounding others, Tom finds himself trapped underground and makes a horrifying discovery as he learns that Lourdes was the mole.

He then leads a team along with Cochise, Kadar and several members of the 2nd Mass on a boat with the weapon mounted onto it and attacks and successfully destroys the Boston tower, bringing down the Espheni planetary defense grid along with it.

Believing the battle to be over for now Tom along with the other members of the 2nd Mass celebrate their victory but are left shocked when the Volm reveal their plans to relocate them to Brazil.

After a minor disagreement, he is held captive and is visited by the Volm commander and explains that after everything that has happened, he along with the other members of the 2nd Mass wish to continue fighting the Espheni to the end and that he, and they wish to liberate the planet.

When Weaver is held in a room next to his, Tom informs him that he is working on a plan to escape from the ghetto, and then reveals that he had been leaving confinement to gather more intelligence on the area, and the skitter locations.

When he also is told of a working radio, he uses it to contact Cochise who tells him that the Espheni power source is offensive in nature, unlike the grid used before, and that he knows where Matt is being held.

With the escape plan now in motion, Tom is now pursued by skitters and Pope is forced to scale the fence when Dingaans hand is injured, meanwhile Hal waits with the ghetto residents in the tunnels.

Now on the run from the Espheni and faced with increasing Beamer patrols, Tom arrives at the Volm hideout in an abandoned warehouse and is immediately greeted by Cochise.

When Anne undergoes memory regression for answers, he spends time by Lexi's side and is joined by Weaver who offers him words of comfort.

With the survivors now gathered, Tom orders them to evacuate to an underground bomb shelter and tells them that the attack won't stop until the Espheni believe they are dead.

Believing that they may be able to use the Beamer to escape, Tom decides to investigate and is implanted with a parasite after touching a panel and tasks Dingaan with removing.

Later that night, Tom and the 2nd Mass decide to gather around a camp fire to mourn the loss of Tector and Lourdes, and after learning that Ben had given some of his spikes to save Maggie, he then talks with Hal and they both notice a strange pulsating light on the Moon.

Tom attacks the Overlord and injects him with a lethal Volm poison which kills him, but before he dies he destroys the ships auto pilot system to prevent them using against the power core.

He then awakens on a bed aboard an unknown spaceship and hears what he believes to be an old radio broadcast, immediately he decides to look around the room and realizes he's in space.

Guided by the Dornia who communicates with him in the image of his deceased wife Rebecca Mason, Tom rallies all the militias across the world into a global resistance to attack the Espheni bases and retake the planet.

Tom takes the weapon and has Anne and resistance fighter Marty work on modifying it so it's non-lethal to humans, but is confronted by the possible return of his daughter Alexis.

Thanks to the modifications Anne and Marty made to it, Tom is immune to the weapon's effects, but the virus passes through his blood into the Espheni queen, killing her.