When an uninvited guest breaks into their headquarters, Team Magma must race against time to make their ambitions become a reality.
In the Team Magma Hideout, the alarms sound as an intruder enters the building. One of the steel doors inside the hideout is sliced open by a Sceptile's Leaf Blade and the intruder is revealed to be Brendan. Brendan and Sceptile proceed through the various sectors of the hideout and defeat Team Magma's Pokémon along the way. His progress is followed through security footage by Tabitha, who informs his boss Maxie about this. Maxie, Tabitha, and a group of Team Magma Grunts head towards the Submarine Explorer 1, which they stole and upgraded. They plan to use it to get through the Seafloor Cavern so they can awaken Groudon.
Before entering the submarine, Maxie encounters Courtney. Maxie proclaims that Team Magma is leaving for the Seafloor Cavern and Tabitha instructs the Grunts to get inside the submarine. As Courtney proceeds to enter the submarine as well, Maxie interrupts her. He tells her that he wants her to stay at the hideout to stop the intruder, who is proceeding further into the hideout by the minute. Courtney says that she understands and watches as Maxie enters the submarine. Courtney tells Maxie that she looks forward to their plans becoming a reality to which Maxie replies they will meet each other again once the mission is over.
As the submarine starts its engines, Courtney has a vision of the future. She sees Primal Groudon coming out of Seafloor Cavern. Primal Groudon charges up a Solar Beam, which it uses to cause massive destruction in the nearby area. It then faces towards Maxie, Tabitha and the Team Magma Grunts and then fires a Solar Beam at them. This ominous vision shocks Courtney, but as she starts to think about what this vision could mean, Brendan and Sceptile show up. Courtney tells Brendan that he is too late and that she will stop him. While doing so, the Submarine Explorer 1 dives underwater. Courtney sends out her Camerupt for battle and laughs as she proclaims she wants to analyze Brendan.