Sixth grade was an epic failure for Jake Herndon. He’s hoping seventh grade will be, in the words of his guardian Uncle Gabe, “the Big Do-Over.” His new start begins with an event called Summer Sleepover, a team-building program for incoming university-prep seventh-graders. It’s held at Chicago’s Museum of Science and Industry after hours.
An African-American boy named TJ, a girl from Napal named Lucy and Jake are thrown together during the scavenger hunt. They follow clues, which take them around the museum. As they search together, they become better acquainted.
TJ, like Jake, loves anything movie-, comic book- or Star Wars-related. He’s a germophobe, who frequently uses hand sanitizer, and he’s a fencing champion. Lucy is skilled in martial arts and speaks many languages. TJ and Lucy notice Jake has one blue eye and one gray eye, a condition known as heterochromia iridum. Jake shares that sixth grade was a bust for him, mainly because he began falling asleep suddenly at random times.
Jake knows the museum layout well since Uncle Gabe has worked there in the past. Gabe, who isn’t a blood relative, adopted Jake when he was a baby. Jake is looking for the next clue on his own, when Lucy accidentally attacks him in the dark. Once she realizes who he is, she explains she’s just seen and heard explosions and people running. She even saw a body drop from above.
As they try to figure out what’s happened, they sneak into the new Chicago: Then and Now exhibit that’s set to open soon. It’s been somewhat demolished in the evening’s chaos. As they look around, they find many valuable pieces untouched. It seems the only things missing are items from an Abraham Lincoln case. They examine the fallen body, which belongs to a now-dead security guard. Lucy hands the guard’s handkerchief to Jake to use on his bleeding lip.
Above them, they hear two men talking about how they got the hat but not the gloves. A moment later, Jake discovers the “handkerchief” he’s holding is actually Abraham Lincoln’s gloves. As they hide in an old airplane on display, Lucy takes down one intruder, who turns out to be TJ.
Once TJ regains consciousness, the three kids continue to crawl through the museum in an attempt to escape. They hear voices again, and one man is growing angry that the gloves were not found. The kids make a daring escape by jumping onto a balcony, but not before TJ accidentally drops his nametag.
The kids overhear a phone call and realize the police may be in on the heist. They can’t turn to the authorities for help. They have to find someone they trust, but all of the parents are taking part in a concurrent retreat on a remote island with no cellphone service. Jake takes the kids to his building. He assures them his doorman, Artie, will know who to call.
While in the apartment, Jake hears a surprising answering machine message, confirming that Gabe has a dinner reservation in Springfield the next evening at Club Thirty, but Gabe’s bag for the parent retreat is still in the apartment. The computer’s internet history shows that someone has been looking at articles related to museum heists where Lincoln artifacts were stolen. Confused, the kids decide to take the train to Springfield to find Uncle Gabe. They flee Jake’s building as police officers begin pouring into the lobby.
In Springfield, the kids find themselves near many of the historic Abraham Lincoln sites. They find the building that houses Club Thirty and try to wait inconspicuously for Gabe. Jake is surprised to see Artie, the doorman, there with a woman. Artie looks uncomfortable to see them and is acting strange. They tell him what they’ve seen at the museum. A little later, they see Artie across the restaurant talking to one of the thugs from the museum. The kids run once again, wondering who to trust.
They read that Amanda Haven, governor and presidential frontrunner, will be closing a big parade that evening. They think if they can get close enough, they can tell her what they’ve seen and get her help. They join the parade as horse clean-up crew members and enjoy a performance by fighting Lincoln impersonators before recognizing that one of the governor’s bodyguards is a thug from the museum. Once he spots them, the kids escape into a carnival. He follows them onto the sky tram, and they escape by jumping into a pool used for a carnival act. Jake discovers he’s lost one of Lincoln’s gloves in the process.
With the police on their trail again, Lucy steals a government Jeep. They attempt to escape but are captured. They find themselves in a vehicle with Artie and soldiers carrying assault rifles. Artie says the kids need to trust him, and he explains that he’s working for a deep cover organization. He tells them about the secret Order of the Dark Lantern, which dates back to the Revolutionary War. Members of this group plotted to assassinate Lincoln.
A close friend of Lincoln’s named Pinkerton learned about this order and began a counter-terrorism group called the Union Defense League. As the Lantern members sought their own wealth and power throughout the world, League members fought them. Artie explains that he’s a member of the League today. Jake is alarmed to see the thug from the museum in Artie’s group, until the man pulls off a high-tech mask to reveal he is Uncle Gabe.
Over a meal of military-grade powdered food, Gabe explains that the Lantern today consists of people studying human cloning, planning cyber-attacks and using bio-weapons. The Lantern believes Lincoln left more gold hidden somewhere, and they want to find it by locating a clue in his clothing. They’re searching for what they call the Clavis Magna, which means “great key.”
The kids stay overnight in the League’s hideout for protection. The next day, Lantern members attack the facility. Since none of the artifacts stored at the facility have any connection to Lincoln’s gold, Artie and Gabe can only assume the Lantern is after people, not things. Gabe gets the kids out of the facility to a Civil War-era hideout near Lincoln’s tomb. The League believes Anarchus Kane, the dangerous leader of the Lantern, is planning to break into Lincoln’s tomb and steal the body.
After receiving intel from another soldier, Gabe realizes that Kane isn’t looking for gold or a literal key. For Kane, the Clavis Magna is Lincoln’s DNA. The League has already theorized Kane may be a clone of John Wilkes Booth. Gabe says maybe Kane wants to inject himself with Lincoln’s DNA as well.
While Gabe is gone, the kids wait with Artie in the safe house. Jake mentions having dropped Lincoln’s glove at the carnival and notes it had some of his own blood on it. Artie quickly calls in a Code Red to Gabe. Lantern members begin to infiltrate the safe house. Kane, with an unconscious Gabe in tow, lures Jake to the safe house tower for a battle.
Jake knows he can rile the man by criticizing Booth’s motives. His insults, in combination with his wrestling moves, allow him to capture Kane and hold him over the ledge. After fighting within himself about whether to finish the job and let Kane die, Jake decides to let the man go. League soldiers swoop in and capture Kane, and Gabe regains consciousness.
Once Lucy and TJ are back with their parents, Gabe tells Jake the rest of the story. Gabe is a descendant of Lincoln’s friend, Pinkerton. When Lincoln’s only living grandson was nearly kidnapped by the Lantern, his father asked the League to fake the son’s death. The son and all his descendants after him became league agents. Jake himself is a descendant of Lincoln. When Jake’s agent parents died on a mission, Gabe promised to care for him.
Gabe warns that the Lantern probably found Jake’s DNA on Lincoln’s glove, so the boy will likely be a target in the future. As Jake enjoys his last day of summer with new friends Lucy and TJ, Lantern members are beginning to set their sights on Jake.