Tom's No. 1 priority has become rescuing his son Ben, who is one of the many harnessed children on Earth. It's unclear why the aliens are capturing and controlling these humans; what is clear is that removing the harnesses lead to almost certain death for the children.
Tom and his oldest son, Hal, along with Karen, Dai, Maggie and Anthony, scout a group of harnessed kids from the safety of a rooftop hiding spot. Ben is one of those zombified people, strapped with an alien harness to his back and neck. The children seem to be scavenging scrap metal from an abandoned warehouse, which seems odd to Tom and his fighters. Upon closer examination, the group discovers that the kids are not alone -- they're being rounded up and guarded by a few mechs and skitters.
Upon noticing they're low on ammo and supplies, Anthony suggests they rethink when to attack, as they may only get one shot at it. Before Tom can disagree, Karen accidentally knocks off a roof shingle, drawing the attention of the aliens. The group narrowly escapes, so the rescue mission will have to wait another day.
The resistance fighters return to the 2nd Mass base camp, John F. Kennedy High School, to report back. As we quickly discover, Tom isn't the only worried father. Parents are desperate to find the whereabouts of their missing sons and daughters, hoping that one of the fighters perhaps saw their child among the harnessed slaves. The pleas become overwhelming to the squad, so Anne suggests using a school announcement board as a missing persons board, where family members can post photos and physical information about their loved ones in the hopes that someone has seen them.
Commander Porter, who is in charge of all the Massachusetts regiments (including the 2nd Mass), has arrived at the school a few weeks earlier than scheduled. He briefs the fighters that contingent resistance fighters exist in Chicago, Texas, Oklahoma and California -- Massachusetts now knows they're not alone. The bad news is that alien structures have settled over all major cities, and no one knows what they're here for. Porter wants the fighters to gathering intelligence about the enemy, secure an operating base, collect materials, explosives, motorcycles, cammo gear and create a growing insurgency. Weaver breaks up the fighters into smaller, search-and-rescue teams.
Tom notifies Porter about the harnessed kids they saw earlier that day, including Ben. It seems that at night, they're remain in an abandoned hospital, and by day, they scavenge scrap metal. Porter says that they were able to get harnesses off three kids, but they all died a couple days later. However, a chief surgeon may have an answer, and Porter wants to test the doctor's theory on Ben. Porter knows it's a hard decision to make, but this may be the only chance that Ben and the kids have. Weaver doesn't believe it's a good idea at all; however, Tom says it'll give hope to the rest of the parents if they see a child survive a harness removal. The two men disagree. It's Porter's call, and he wants to save only Ben this time.
These are the hard decisions that fall on Porter's shoulders -- just an old soldier who was set to retire before the invasion began.
Tom meets up with Matt, his youngest son. The child asks about his brother Ben, and Tom says he found him. Matt seems depressed and tells his father that he heard about how the harnessed kids die with the apparatuses are removed. Tom tries to comfort Matt by telling him there's a doctor who has figured out a way of removing the harnesses safely. Technically, this isn't true since the theory has yet to be tested but hope is hope.
Meanwhile, the school is also being used as a makeshift jail, with John Pope as the only real prisoner. This criminal tried to shake down the 2nd Mass and steal its weaponry, but Weaver and his soldiers eventually caught him and made him join the resistance. He may be safe from the aliens but he's now under the watchful eye of Weaver and his men. Uncle Scott offers food to the prisoner, but Pope spits it out immediately. He may be locked up but looks like he still has a discerning palette. He offers Scott a cooking lesson before he shoves the plate of chicken and rice back in his captor's face.
Turns out that Pope is a pretty talented chef, which Maggie, a former member of his gang, can attest to. Uncle Scott suggests making Pope head cook. Weaver offers the job to Pope who hesitates based on the supplies he's given. Weaver offers him two choices: prepare food with basic equipment and rations or go back to lockup. Pope chooses the former.
While stationed at basecamp, Tom seeks the guidance of a trusted medical professional, like Anne. She says the surgeon set to remove the harness seems capable and knowledgeable. When Tom hears the surgeon's name, Michael Harris, his ears perk up. It turns out that he knows Dr. Harris, pre-invasion.
The two men meet and participate in what seems like a forced conversation. We discover that Dr. Harris and Tom's wife, Rebecca, were together around the time of the invasion. We don't know the details about their relationship, but Dr. Harris tells Tom what happened that night. He says that he and Rebecca foraged for a couple of hours and then decided they'd be more efficient if they split up. At that point, alien airships started pounding the area, and though he tried to get to Rebecca, he couldn't. The second wave of the invasion began, so Dr. Harris hid in a collapsed house, eventually passing out. He says resistance fighters found him, which led him to the opportunity of becoming their medical officer. He tells Tom that he's sorry about the death of his wife, Rebecca.
Tom replies by telling the doctor that Ben is harnessed. He also says that after the Masons had found Rebecca's body, they went to look for Dr. Harris, but there were skitter patrols everywhere. The doctor understands and offers the only consolation he can: He couldn't save Rebecca's life but maybe he can save Ben's.
Later, Tom's small crew head out to rescue the harnessed kids. They spot them again, scavenging scrap metal at the building. While Dai waits in the getaway car, the rest of the team heads out in the streets. As they patrol, Mike sees his missing son, Ricky, among the enslaved children. Mike blows his cover when a burst of adrenaline rushes over him. However, by giving away his location, he puts the entire team at risk. He runs over to a harnessed Ricky, who seems totally unaware of his father's identity. This sets off a chaotic chain reaction. Before the mech has time to strike the reunited pair, Tom sets off an explosive. The squad grabs Ricky and loads him in the truck.
Since the mission has already been blown, it's now or never for Tom to rescue Ben. However, an explosive causes Tom to lose consciousness, and it's up to Karen and Hal to defend the group. They try to outrun the mech but get caught.
Tom wakes up in a building and realizes Dai and his squad abandoned position without Hal and Karen. Now he has two sons missing. He directs his anger at Mike, who blew the entire plan when he saw his child, Ricky, among the harnessed children. Tom decides that he's going back for Hal and Karen.
He makes his way through an abandoned hallway, but it turns out the hallway isn't abandoned at all. A skitter makes a surprise attack, barely giving Tom enough time to get his bearings. During the struggle, he manages to take out one of the alien's limbs, and eventually overpowers his assailant. His frustrations over the day's failed mission appear as he brutally takes on the extraterrestrial.
Later that day, Porter and Weaver discover that Ricky, not Ben, is the harnessed child who was rescued. Though Tom may not have his son, he does return to base camp with something -- a skitter. He drags the injured alien, from the earlier hallway attack, through the high school and calls it his prisoner of war. After drawing the attention of the people around him, Tom demands that he get the opportunity to go back and rescue both of his sons and Karen.
Matt overhears Tom, realizing he now has two missing brothers. He confidently tells his dad to go and bring back the rest of their family, sealing his statement with a simple hug.
Meanwhile, a confused Hal awakens to find the remaining harnessed kids hovering over an unconscious Karen, pulling her into their ranks. One of those kids is Ben. A mech shines a light on Hal, who is still unsure of what is happening (or about to happen). An additional five harnessed children surround him, as well as a skitter who points at Hal then the row of kids. The five enslaved children just stand there, mindless to what's going on. Hal realizes what's about to happen, but it's too late -- this is an assassination line. The mech shoots and kills all the harnessed prisoners.
While Hal's fate is up in the air, Dr. Harris attempts to perform a very difficult, and unproven, surgery to remove Ricky's harness. Ricky, who has cystic fibrosis, lays face first on the gurney. Dr. Harris, assisted by Anne and Lourdes, wants to expose as much of the harness needle as possible in order for a successful recovery. Based on trial and error of previous surgeries, Dr. Harris uses a blow torch on the needles. Though it's a tricky procedure, Ricky remains alive after the harness has been removed.
Later that night, Tom heads back toward the attack site and sees Hal, wandering aimlessly. An exhausted Hal says that Ben and the other children took Karen to the skitter. He constantly asks why his dad left them. Tom begs for forgiveness, telling him how Mike ruined the rescue mission, and that he would have never left him and Karen otherwise. Hal loses control over his emotions when he tells his father that the mech killed five of the harnessed children, though not Ben. Tom's surprised to hear that the aliens just let Hal go unscathed, but realizes this is a military tactic -- they're sending a message to the resistance.
Back at base camp, the fighters use the prison cell for the injured skitter that Tom brought back earlier. Porter wants to keep the alien alive in order to study its physiology, which is why he's keeping a Dr. Harris around for the next few weeks.
After Tom and Hal return to camp, the former stops by the "hospital" to see how Ricky is doing. Anne tells him that things are good so far, but her hopeful mood quickly changes when she hears that Karen has been captured. The silver lining for the time being is that at least the squad knows how to remove harnesses, which will be helpful for future rescue missions.
Tom leaves to talk to Dr. Harris, who is observing the imprisoned skitter with a bottle of scotch in hand. The doctor makes small talk with Tom, saying that those people who survived the first wave of the invasion aren't the best of mankind, that many of them stayed alive by being cowards. This statement sparks something in Tom who asks Dr. Harris, point blank, if he survived by hiding. He wants to know how his wife, Rebecca, ended up alone and dead if the doctor was with her. He accuses Harris of abandoning his wife to save himself. He comes to this theory because when he found her body, those few months ago, she was still holding a duffle bag full of provisions -- too heavy for one person to carry. She was supposedly with Dr. Harris, who, it seems, left her alone to save his own life.
Dr. Harris tries to justify leaving Rebecca, but Tom can't hear another word and punches the surgeon in the face. An injured (and obviously drunk) Harris responds that Tom must feel guilty. He says that Rebecca told him that fateful morning that it was actually Tom's turn to gather supplies, but she didn't want to wake him and instead, went out in his place. Essentially, her death is on Tom's hands just as much as it is on the doctor's.
Harris says that they may not have been able to save Rebecca's life, but they can work together to save Ben's. The two men will try to get over their personal issues in order to benefit mankind.
Before Tom goes to sleep next to Matt and Hal, he stops by the missing persons board and hangs a photo of Ben. He sheds a tear for his missing son as well as all the other harnessed children.
Though many have turned in for the night, there are two just waking up. A recovering Ricky and the imprisoned skitter seem to share some type of connection -- as both regain consciousness simultaneously while everyone else sleeps.