Charlie is being held on the ground as an unknown Militia officer prepares to brand her with Monroe's M. Flash back two days: Charlie and the gang hide near the side of a road as a Militia wagon carrying a teenaged prisoner passes. Thinking this kid is just like Danny, Charlie loosens her knife, but Miles stops her - they can't go around rescuing random strangers! Further down the road, Charlie spies a little kid lying unconscious in the middle of the road. When she runs to help, the kid jumps up and runs off, signaling to several other kids, who pop out of the woodwork with bows and arrows. Fourteen-year-old Michael demands to know where Peter is as young Jack checks Charlie for "burn marks." Charlie realizes the Militia captured Peter, Michael's brother, and furthermore, these kids don't know what the Militia is. When Miles demands to know where the kids' parents are, Michael admits they don't have any.
Michael whistles, bringing at least 20 kids of all shapes and sizes out of the abandoned apartment building where they've been squatting. Michael is ready to head out after Peter, but Miles demands to know what happened to his parents. Michael explains: a long time ago, his parents hid the kids in the basement when men with burn marks came to kill them because of their tattered American flag. The kids waited and waited, but when their parents never came back, they went outside to find all the adults dead. Peter has kept them alive since then. When Michael insists on going after him, Charlie promises to get Peter back, and everyone is surprised when Miles agrees with her. Telling Michael to stay put, Charlie et al take off, promising to return with Peter.
Danny and Rachel share a meal in her quarters at Independence Hall. Danny can't understand why Rachel is playing it so cool; he wants to try to escape, but Rachel will only say the situation could be a lot worse. Suddenly, a guard summons her to meet with Monroe and Neville, who are upset that they've yet to find a single pendant. The addresses she gave them for her former colleagues have yielded nothing... except Dr. Bradley Jaffe, whom they've had in custody for three weeks. Understanding Neville has been torturing Jaffe in hopes of locating his pendant, Rachel offers to talk to him.
Rachel flashes back to three years before the blackout, when she was six months pregnant. Assistant Defense Secretary Flynn stands in an incubator filled with electronic devices in the office/lab Rachel shares with Ben, Grace and Dr. Bradley Jaffe. Oddly, Ben and Flynn are speaking by telephone. Ben explains the project to generate clean, low-cost electricity that he and his partners have been working on has failed. Instead of generating electricity, they've succeeded in inhibiting it. He demonstrates by instantly shutting off power to all devices in the incubator. Walking into the middle of the demonstration, an irate Rachel pulls Ben aside. How could he not tell her that he was going to the DOD?! What if they use the device as a weapon? But Ben has thought it through; his first priority is keeping their fledgling company alive - the DOD is a lifeline.
Miles isn't happy to be tracking the Militia once again, especially since there are not one set of wagon treads to follow, but more like 12. Hanging back, Aaron complains to Nora. Not only does he hate kids, but also he's unable to comprehend how hard-hearted Miles would consent to saving Peter. Nora gets it; clearly all the lost children became orphans when Miles was in charge of the Militia. Suddenly, a twig snaps, and within seconds, Miles pulls Michael out of the bushes. Michael explains that just like Charlie, there's no way he wouldn't go after his brother. When Charlie consents to let him stay, he whistles, bringing three more orphans out of the trees.
The wagon containing Peter and his fellow prisoner, 15-year-old Audrey, pulls up at a camp on the banks of the Ohio River, where a freighter is moored offshore. Meanwhile, Charlie, Miles and the gang stop for water. One of the kids, Skip, pulls Aaron's necklace out of his rucksack. Annoyed and anxious, Aaron chases him down, and Miles takes note - why is Aaron sweating over a necklace? Just then Nora runs up, dragging Miles to a sight he has to see at the base of an old lighthouse - the freighter. Miles knows it's a "conscription facility," aka a soldier factory. Kids go in and get reeducated, and soldiers come out. Rescuing Peter off the back of a wagon is one thing, but storming the freighter - that's impossible.
Sitting in a prison cell, Rachel flashes back to three months before the blackout. Leaving the office, Rachel stumbles to the ground in tremendous pain - something's wrong with the baby. After an ultrasound, her doctor offers a terrible choice. Since Ben and Rachel's son is missing a blood vessel that helps pump blood to the lungs (truncus arteriosus), they could induce labor and operate on him now. Or they can wait until the baby comes to term. Whatever they decide to do, it's unlikely their son will survive.
Rachel is sitting in her cell in Philadelphia when a prisoner is dragged in and dumped in the cell next door - it's Bradley Jaffe, who tells Rachel that he thought she was dead. Rachel asks about his pendant; they do have a few friends in Philadelphia, undercover rebels posing as guards. If he does know where his pendant is, they could go get it, keep it safe. Plus Monroe can't make Jaffe talk if he doesn't know where his pendant is. But what Jaffe wants to know is how Monroe knew about the pendants in the first place...? Suspicious, Jaffe tells Rachel that he's not going to tell anyone anything. Their conversation is over.
Charlie hatches a plan: she wants to masquerade as a recruit, board the freighter and rescue Peter. Miles tells her to forget it, then explains that whatever happens on that boat is his fault - not to mention what happened to Peter's parents and Danny. Charlie doesn't care; though she has serious doubts about the likelihood of retrieving Danny, at least they have a chance to help the orphans. Despite his best judgment, Miles gives his consent - but with a warning. If Charlie's going to get Peter back, she'll need a master key, and that's going to hurt. That night at dusk, Charlie is sitting alone by a campfire when Peter's captors drive by in their Militia wagon. It's not long before they have cracked her across the jaw and taken her into custody.
It's night when a guard dumps Jaffe in Rachel's room. Jaffe immediately lays into her for working for Monroe. Rachel explains that she's a prisoner, and Monroe's intent is to kill Jaffe. Jaffe maintains there are worse things than dying, like betraying all your friends. Rachel insists that in all her years as a prisoner, she's never said a word - until Monroe threatened to torture her son. So yes, there are worse things than dying. Nevertheless, Jaffe knows that if they hand Monroe the pendants, they're talking about millions of lives. Having silently entered the room, Neville cautions that it's easy to be self-righteous when someone else's child is on the hook. That's when a guard brings in Jaffe's daughter Eve, causing Rachel to recoil in horror. Jaffe immediately assumes it's all Rachel's fault, but she insists she didn't know.
When Neville insists he's going to keep Eve safe, Rachel begs him to let her go. Instead, Neville outs her for telling them about Jaffe in the first place. After that, it was easy to find Eve. As he's pulled out of the room, Jaffe screams to a hysterical Rachel, "How could you do this!?" Meanwhile, Charlie and Peter stand with 30 other recruits before Lieutenant Slotnick, who welcomes them to the Militia with a propaganda speech. When a scared boy tells Slotnick that he just wants to go home, Slotnick lets him leave, inviting others to join in - they're free. Free that is until Slotnick subjects the boy to a brutal beating in front of the others, leaving him sobbing on the floor. It's not long before the recruits are taken below decks and assigned to quarters. Noting Peter's room location, Charlie makes sure Slotnick is watching when she picks a fight with beefy recruit Boggs - who knocks her out cold.
Aaron, Charlie and Nora wait impatiently for Charlie, watching the freighter from the lighthouse. Back on the freighter, Charlie comes to in the infirmary, just as a medic is about to inject her with a syringe. Spying the key ring hanging around his neck, Charlie punches the guy, grabs the syringe and plunges it into his jugular. Sadly, Slotnick's there to stop her from leaving with the keys. Deciding Charlie is two hours late, Miles can't wait any longer. He grabs Nora and heads for the freighter, leaving Michael and the other kids with Aaron, who's none too happy to become a babysitter. Then we return to the first scene of this episode. Slotnick smiles diabolically as the M brand sizzles into Charlie's flesh.
Charlie is locked in a cell recovering from her tattoo ordeal when Miles and Nora take out a guard and board the freighter. It's not long before another guard sounds an alarm, forcing Miles and Nora to swordfight their way below decks, calling out for Charlie. Miles is devastated to see Charlie's brand, but she's focused on rescuing Peter. Back at the lighthouse, Aaron has just discovered that Michael's missing when footsteps can be heard on the floor above them. The kids are quick to hide - and help Aaron hide - as the Militia searches the building. Suddenly, Aaron's pendant activates, the lighthouse whirrs to life - and the giant light turns on!
Charlie, Miles and Nora are just leaving the freighter with Peter when Slotnick shows up, his knife to Michael's neck. Suddenly, the deck of the freighter is engulfed in the lighthouse's blinding light. After the initial shock wears off, Miles uses the opportunity to head butt Slotnick, free the kids and start a swordfight, allowing Charlie to finish Slotnick off. Back at the lighthouse, the pendant's light extinguishes, taking the lighthouse's power with it. When the Militia men get too near their hiding place, Aaron saves the kids, taking the soldiers out with a pipe.
It's early in the morning when Monroe pays his next visit to Rachel. Riders are on their way to Jaffe's house to retrieve his pendant. As soon as it's in Monroe's possession, he tells Rachel, Jaffe and his daughter will be free to go. But one thing's still bugging Monroe: how did Rachel and her people shut down the power to begin with? Rachel thinks it makes no difference, as long as she can turn it back on again. As Monroe leaves, Rachel flashes back to three years before the blackout. It's night when Flynn accosts her outside the office building. He apologizes for overstepping, but he heard about her unborn son's problem and arranged for a spot in the now full fetoscopic trial at Columbia. Why not give her baby a fighting chance? Rachel knows this is a Faustian bargain, and Flynn isn't going to name his price... at least not now.
The next morning, Aaron waits on the dock with the kids as Charlie, Miles and Nora row up in a boat with Peter and Michael. The kids run up, overjoyed to see Peter; even Nora earns a hug. But Miles is all business. He makes a beeline for Aaron, demanding to know how the lighthouse could have possibly lit up last night. Aaron reluctantly pulls the pendant out of his pocket. Even though he's not sure what happened, he knows the pendant sometimes turns the power back on, and yes, it came from Ben. Incensed Aaron never said anything about it, Miles demands he turn over the pendant, so he can smash it, threatening to beat him unconscious if he doesn't comply. Just then Charlie runs up, demanding to know what happened with the lighthouse. Aaron shows her the pendant and starts to explain the whole story...
The door to Grace's cell opens, and though we can't see her captor at first, we know it's Randall Flynn. When she asks to be let free, Flynn reminds her they both know that can't happen; it's too dangerous. Besides, he just wants to be friends...