Sky Attack

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The Nidorient Express is under attack. In the S-class Trainer Lounge, Nautilus helmsman Terronius Chunder reveals himself, having been posing as one of the other S class trainers. He immediately begins knocking out the powerful trainers of the lounge with a noxious Weezing. Theo finds Kenny in the lounge, and together with Theo's Meditite and Kenny's Honchcrow, the pair subdue Terronius. Accompanied by Enya and Melissa, Theo and Kenny head for the ChUrch of SlaSlo's train car. At the entrance to the ChUrch car, Kenny & Theo see that the acolytes and Paladins of the ChUrch have erected a rudimentary barricade and will not let anyone pass. Theo's Togekiss and Bowtie the Dartrix subdue the acolytes peacefully, before Kenny convinces the Paladins to let them through, with the help of Enya and her parents.

Meanwhile, Brandi deals with the explosion in the engine room. The powerful electro blast has torn a hole in the side of the train, and the Meltan working on the engine are in danger of being ripped outside of the speeding vehicle. Brandi releases the Meltan from their bondage, defeating Train Chief Arnod in the process, and sealing the hole in the engine. Brandi organises the train inspectors to defend the train from the Nautilus troops descending from the sky, riding enormous Gyarados, each launched from their capital ship, which hovers in stormy silhouette against the ghastly sky, suspended by a giant inflated Octillery. Brandi notices one of the Gyarados deposit a mysterious figure in a Dustox-like helmet onto the train, and she decides to follow them. Brandi pursues the Dustox-helmeted figure, and discovers him to be her ex-boyfriend, captured Pokemon Champion Gary Smoke. Gary warns Brandi not to get in his way- he's working with Nautilus under duress, in order to get his Pokemon back, and she is not going to stop him. Brandi, reminding Gary that she currently has more Pokemon than Gary, and could thus defeat him with ease, convinces him that they should attempt to break into the ChUrch car together.

Theo and Kenny defeat two Nautilus grunts, before searching frantically for a way to reach the secret chamber beneath, which presumably holds what ever Nautilus is after. during the search, Kenny discovers a tiny human, who upon closer inspection, turns out to be Cainan, having escaped from Mrs W in the prison section above by using a minimize potion on themselves, and has been hiding down here since. Cainan, once maximized by a potion hastily made by Theo and Kenny, explains the only way to reach the lower level of the ChUrch car is with a Slowpoke Tail. Kenny's Magikarp, Moustache, convinces a Slowpoke living in the ChUrch car to accompany the team and provide its tail by painting a magnificent portrait. Theo, Cainan, Kenny and Melissa descend into the secret chamber beneath the ChUrch car. Below, the see Mrs W, her Paladin, known simply as Prime, and her terrified-looking Malamar in the midst of a ritual. Theo explains the ritual's purpose- to destroy whatever is at its center, and that a sacrificial Pokemon is required to complete it- in this case, the Malamar. At the center is a giant metallic diving bell with unknown contents. Simultaneously, Brandi and Gary break in through the outside of the carriage- Wimpy smashing through the wall with a monstrous pound. Exposed to the elements, the sanctity of the ritual is shattered, and the Malamar makes a dash for it; firing a dark pulse which incapacitates Brandi in its escape, causing Gary to faint due to his newfound fear of blood. In order to prevent the diving bell falling into Nautilus hands, Theo proposes altering the ritual to one of teleportation rather than destruction. Desperate, Mrs W agrees.

However, the ritual goes awry when Cainan refuses to allow the sacrifice of the Slowpoke. The diving bell, along with the inhabitants and contents of the secret ChUrch car room, are accidentally teleported onto the deck of the Team Nautilus capital ship. Kenny is the first to awaken on deck, and sees a nebulous mist forming from within the diving bell. A Spiritomb emerges, and encourages Kenny to 'prove himself' if he wishes to obtain that which the Spiritomb possesses- the second tome. Kenny harnesses his powers in a controlled manner, and fires a blast at the billowing ghost-type, watching it vanish in a haze of smoke before his eyes. In its place comes the second tome, and a mirage-like vision depicting an older version of himself binding the Spiritomb to the tome. In addition, the egg Kenny discovered in his own Mind Palace begins to hatch, birthing a tiny baby Spiritomb.

Now in possession of the tome, Kenny's compatriots begin to wake up. The day is not won, however, as Alyza, the captain and leader of Team Nautilus, crests the deck of her own ship on a Mega Gyarados, and demands Kenny give her the tome. a vicious battle ensues on the deck, and in the melee, Kenny is able to trick Alyza into pursuing a fake tome, not before Alyza covers the ship in a thick fog. Kenny enters Alyza's Mind Palace, and helps her quell the rage within her sparked by Frey unlocking Alyza's weather-based powers by telling her to think of her family. Her mania subdued, Alyza concedes defeat, having lost the desire to sow chaos, and pursue a goal that was never truly hers to begin with.

Mrs W, transported onto the deck of the ship with everybody else, demands that the ChUrch retake custody of both the tome under Kenny's possession, and the one stolen by Team Nautilus. Not seeing how violence isn't the answer, Theo attempts to go after Mrs W with a Scyther Sword, before Brandi stops them. Instead, Theo challenges Mrs W to a Slowking Duel, a trivia-style event, treated with insane reverence from dedicated ChUrch members, moderated by Prime. Prime scans Theo Brandi and Kenny, and Brandi learns her surname- Brandi Flash. Besting Mrs W with a male Combee-based question, Theo claims right over the tomes before banishing her from the ship.

Gary Smoke, seeing the potential in Wimpy he had not seen before, asks the Buneary if he wants to join the team of the Pokemon Champion himself. Brandi, not wanting to decide for her partner Pokemon, leaves Wimpy to decide whether he leaves with Gary, or stays with her. Wimpy makes up his mind to go with Gary- before returning to Brandi, hugging her, and evolves into a Lopunny.

As Alyza's summoned storm clouds part, Cassius Flash and Calico, riding on an Altaria, land on the ship. Cassius warns everyone that Operation Ironclaw- a division of the Pokemon League are on their way, with orders to destroy the ship and all inside. If Theo, Kenny and Brandi want to get away without questions being asked and their assets being seized, now is the time to go. Brandi questions Cassius Flash, and under scrutiny, he not only reveals that he is her uncle, but that he knows what happened to her father. Dealeo the Sealeo, Brandi's mother's loyal companion is more than a family Pokemon. he is Brandi's Pokepowered father- Leo, transformed into a Pokemon after an encounter with Team Mystic's Frey. Brandi is shell-shocked, but, still ashamed by his inability to protect his brother-in-law, Cassius departs. Kenny's Magikarp evolves into an artistically-inclined Gyarados, but even the magnificent water dragon is unable to catch up to Cassius's Altaria, and he disappears with many of Brandi's questions unanswered.

Theo recovers the second ChUrch tome from the treasure room in the belly of the ship, after Calico preforms a Nautilus Dance routine to unlock the vault. in the vault, Theo encounters Adri Formonsk, who has apparently been on the Nautilus ship for some time, and Ellie the newly-evolved Manectric. Theo convinces Adri to stay on the ship as Theo's research assistant, in order to research the tomes they now have access to. with an assembled crew including Terronius Chunder, Cainan, Adri, and Calico, our heroes seize control of the Team Nautilus flying ship, and jet off towards Surfloat Town, before the Pokemon League can reach the site of the Nidorient Express incident. Kenny places Alyza under house arrest back in Surfloat, before dropping off Melissa in Combover Town with a letter, written by Kenny, to his still-comatose sister, Dora. With two of the sacred ChUrch tomes under their possession, the trio and their crew sail over the horizon, mindful of the challenges yet to come.