The action takes place in two locations:
John (#4), Sam (his best friend), Nine and Five are in New York, after Setrakus Ra has basically destroyed the city. Six, Mariana (#7), Adam (Mogodorian traitor and supporter of Lorien) are in Mexico, having met “The Entity” (the spiritual embodiment of Lorien). Ella (#10) is still being held on board the Mog ship Anubis, where S. Ra is working on turning her into a Mog. He still has a charm on her, causing any injuries on his body to only appear on hers.
Sam has just developed a Legacy (telekenesis) and as he and John are running for their lives in New York, they meet Daniela, a native New York teen who has also developed telekeneis. They meet up with FBI Agent Walker, who urges them to work with the government to come up with a way to defeat the Mogs. John is skeptical, as the gov’t have not exactly been supportive thus far. In the midst of the action, John is contacted telepathically by Ella. Her powers have grown stronger, and she is able to communicate from a greater distance, and is capable of seeing the future, although she knows it can be changed. When he awakes, he and Sam are given satellite phones, and they call Six and Sarah, who is still somewhere with her old friend Mark, trying to gather information. John learns that Sarah made a YouTube video, featuring him, begging the people of earth to help Lorien, and that’s why John is suddenly recognized by people. Shortly thereafter, they learn Five is holding Nine at the Statue of Liberty, and demands Sam and John find him there. Five, who is severely injured, clearly wants to commit suicide by way of John, but John knocks him out, removes the metal and rubber balls that allow him to turn into metal or rubber and heals both Five and Nine. Just then, a huge Mogodorian creature emerges from the sea, attacking everyone in sight.
In Mexico, Six, Adam and Mariana discover there ship has been disabled by Mog warrior Phiri Dun-ra, who has disabled all the other ships in the area so they can’t scavenge for parts. They hold her prisoner while they try to figure out what to do. Sam calls and tells Six that he and at least one other person have developed Legacies, so Six et al know that whatver happened with the Entity, it had far-reaching effects. John then asks Adam what he knows about Mog ships that might be useful to the US gov’t. John tells them of Ella’s vision of the Anubis coming to Mexico to capture the Lorien temple, and even though Ella said they should run, he tells them he’ll try to get to US military to come down and help. Six, Adam and Mariana begin planning a defense, and Sarah and Mark show up in a Lorien ship, powered by Lexa, a Lorien who’s been in the background all this time. She has no Legacies, but wants to help. They continue preparing, but the Anubis arrives early and targets the temple; S. Ra doesn’ want the temple, he wants to destroy it. He’s using a weapon based on Loric energy, and while he is using it, Ella appears and throws herself into the energy stream. Suddenly, anyone with a Loric Legacy (including S. Ra), loses consciousness.
They all come to in a library room, and realize this is all a telepathic experience controlled by the Ella, with the help of the Entity’s energy. She leads them to a large stadium room Everyone is shown the history of S. Ra and Pittacus Lore: they were friends, but S. Ra became obsessed with playing with the genetics of Loriens and Mogs, and was banished for it; S. Ra was Loric. After the vision, suddenly everyone on Earth who has been granted a Legacy appears in the room. John tries to explain what’s happening, and asks for their help. People are confused, but some are eager to help. S. Ra escapes his bonds and swears to hunt down all those people. Everyone regains consciousness and learns only a second has passed, and they are still locked in battle (with the Mog sea monster in New York, and S. Ra in Mexico.)
Six is determined to kill S. Ra, now that Ella is (seemingly) dead and beyond injury, though no new scar has appeared on anyone’s ankle. Mog soldiers drag him back to the Anubis, and Six isn’t sure what condition he’s in, though she figures it must be bad since she just impaled him with a large metal pole. Everyone board’s Lexa’s ship to make their escape. Meanwhile, Mariana is seriously injured , leaving her unable to attend to anyone else’s injuries, especially Sarah’s, which are severe. Ella is also on board, but in no condition to do much of anything.
In New York, John discovers he has developed Ximic, a Legacy that allows him to absorb the Legacies of others. He, Sam, Five, Nine and Daniela battle the creature; Daniela and John eventually bring it down with Daniela’s new Legacy, turning things to stone. Shortly after the creature is down, John’s phone rings. It is Sarah, calling from Mexico. She tells him she loves him, and he should keep fighting, and she dies, with Six, Mark and Adam looking on.