Villain Arc

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The Villain Arc (Japanese: 悪の組織編) is a storyline available in Pokémon Masters EX as part of its Main Story (Japanese: メインストーリー Main Story) which follows on from the events of the PML Arc. In the Villain Arc, Scottie / Bettie find out and thwart the plans of Team Rocket with the assistance of their friends on Pasio.

As with the PML Arc, each chapter is unlocked once the previous one is completed and battles are available in Normal and Hard difficulties. All Normal difficulty battles provide 30 Gems as a First-Time Reward, while Hard difficulty battles reward the player with 100 Gems upon defeating the stage for the first time. The recommended level for the Villain Arc is level 30.

The script for the Villain Arc can be found here.

Kanto: Team Rocket Returns

Battles

Name	Difficulty	Trainer	Pokémon			Completion Rewards
Name	Difficulty	Trainer	Left	Middle	Right	Completion Rewards
Challenge the Rocket Grunts: Part 1	Normal	Team Rocket Grunt	Pidgey Weakness:	Fearow Weakness:	Farfetch'd Weakness:	150 coins 2★ Level-Up Manual
Challenge the Rocket Grunts: Part 2	Normal	Team Rocket Grunt	Zubat Weakness:	Venomoth Weakness:	Pinsir Weakness:	240 coins 2★ Level-Up Manual
Challenge the Rocket Grunts: Part 3	Normal	Team Rocket Grunt	Arcanine Weakness:	Ninetales Weakness:	Magmar Weakness:	450 coins 2★ Level-Up Manual
Challenge Giovanni: Part 1	Normal	Giovanni	Golbat Weakness:	Mewtwo Weakness:	Beedrill Weakness:	900 coins 2★ Level-Up Manual
Challenge the Rocket Grunts: Part 4	Normal	Team Rocket Grunt	Kabuto Weakness:	Dewgong Weakness:	Seaking Weakness:	1,400 coins 2★ Level-Up Manual
Challenge the Rocket Grunts: Part 5	Normal	Team Rocket Grunt	Seel Weakness:	Kabutops Weakness:	Starmie Weakness:	1,900 coins 2★ Level-Up Manual
Challenge the Rocket Grunts: Part 6	Normal	Team Rocket Grunt	Graveler Weakness:	Sandslash Weakness:	Marowak Weakness:	2,400 coins 2★ Level-Up Manual
Challenge Giovanni: Part 2	Normal	Giovanni	Omastar Weakness:	Mega Mewtwo Y Weakness:	Lapras Weakness:	2,620 coins ★ Level-Up Manual
Challenge Giovanni: Part 2	Hard	Giovanni	Omastar Weakness:	Mega Mewtwo Y Weakness:	Lapras Weakness:	2,770 coins 2★ Level-Up Manual

Sinnoh: Dreaming in Darkness

This chapter following the end of Team Rocket Returns.

Plot

The episode begins with Cyrus waking up from a never-ending darkness caused by Darkrai. Wanting to live in this never-ending ideal void, Cyrus states he will learn more about sync stones and Sygna Suits to harness their power.

At the laboratory, Professor Bellis informs the player that the International Police have started their investigations on Pasio, including into recent issues with Team Galactic. Barry leaves to stop Team Galactic, while Lucas and Dawn go to inform Cynthia.

At some ruins, Lucas and Dawn arrive and find Cynthia. Cynthia tells them that Legendary Pokémon seem to have been appearing at these ruins, and that Giratina appears to be interested in the traces of other Pokémon that have come here. Dialga then appears suddenly before disappearing, and Lucas wonders if it was trying to tell them something. Dawn then goes on to report to Cynthia about Team Galactic's operations on Pasio. A mysterious man spots the cave and enters the Team Galactic hideout disguised as Grunt with Croagunk.

At Centra City, Brock and Erika confront and defeat Team Galactic commanders Jupiter, Mas and Saturn who have been trapping other Trainers in a nightmare. Barry arrives, and the team head back to Bellis's lab to update Cynthia, Dawn and Lucas on this mysterious phenomenon. They speculate that Team Galactic appear to be harnessing Darkrai's power, before Professor Bellis reports to the team that the International Police have found Team Galactic's hideout. Near the hideout, Cynthia, Lucas and Dawn meet Barry. Cynthia suggests that the team should split out with her being alone. That means Lucas, Dawn, and Barry will go as a group.

Inside the hideout, the team battling against three Grunts. The other Grunt, which is mystery man that was with Croagunk, commands it to stop the other Grunt's Pokémon. Later, these Pokémon has fainted and the Grunts retreated. The mystery man who was actually Looker, removes his Grunt disguise and introduced himself. He was sent to International Police to investigate Pasio. Looker left and he disguises as Grunt again. Cynthia alone met with commanders, challenges their Pokémon with Giratina and wins. She warns the commanders about consequences what Cyrus will do. Saturn say that he is seeking more power to create a brand-new universe.

Lucas, Dawn, and Barry met with Cyrus, who now have both Dialga and Palkia and command to get them. Dialga disobey Cyrus. Palkia attacks it, and Lucas wants him to stop this. Cyrus say he wants to create a world that got rid of incomplete spirit and where feelings no longer exist with all human spirit must be erased, with his conversation was heard at the lab. At hideout, Cynthia left the commanders, as they are questioning him. Cyrus become victorious on the team's Pokémon. Lucas's sync stone is reacting what Dialga has been waiting for this and he forms the sync pair with it. Lucas and Dialga use their sync move against Cyrus's Palkia and defeated Cyrus. After the battle, Cyrus with Darkrai were vanished. Looker inform team that Grunts were asleep due to Darkrai powers.

A few days later, at the lab, the team discuss that Cyrus's plans has been putting into action and all sync pairs all over Pasio are falling asleep, having terrible nightmares and no waking up. Looker mentions that the affected sync pairs are getting treated at the Pokémon Center. Dawn arrives and she informed that she was able to wake up all affected sync pairs with Cresselia's power.

Cyrus in his sygna suit appears inside the Darkrai's Dark Void and claim that it is the ideal world he seek.

At the Bellis Lab, Dawn dresses herself in sygna suit to match Cresselia's colors. Professors Sycamore and Bellis arrive to the lab and report that Darkrai's nightmare is taken over with Sycamore falls asleep because of it.

Cynthia and company arrive to Centra City to see the sync pairs fall asleep. They thought that Darkrai's power overpowering Cresselia's. They later returned to the lab, because they can also be asleep. The commanders arrive to the lab to help the company finding Cyrus.

They found the asleep grunt, which actually is disguised Looker. He found the whereabouts of Cyrus. The group arrive to the cave and see Darkrai. They entered the Dark Void, with Dawn's Cresselia using power to wake up Cyrus from nightmare. They battled him and won. After that, they told Cyrus about how important feelings and bonds are. Cyrus managed to understand it and leaves with his commanders. Meanwhile, Giovanni appears at the scene after Cyrus leave and calls his loyal subordinates to preparing Team Rocket's Revival. At the lab, the group hope Cyrus will change.

Battles

Name	Difficulty	Trainer	Pokémon			Completion Rewards
Name	Difficulty	Trainer	Left	Middle	Right	Completion Rewards
Challenge the Galactic Grunts: Part 1	Normal	Team Galactic Grunt	Vibrava Weakness:	Noivern Weakness:	Dragonair Weakness:	150 coins 2★ Level-Up Manual
Challenge the Galactic Grunts: Part 2	Normal					240 coins 2★ Level-Up Manual
Challenge the Galactic Grunts: Part 3	Normal					450 coins 2★ Level-Up Manual
Challenge Cyrus: Part 1	Normal	Cyrus	Flygon Weakness:	Palkia Weakness:	File:Masters445.png Garchomp Weakness:	900 coins 2★ Level-Up Manual
Challenge the Galactic Grunts: Part 4	Normal	Team Galactic Grunt	Sneasel Weakness:	Absol Weakness:	Mightyena Weakness:	1400 coins 2★ Level-Up Manual
Challenge the Galactic Grunts: Part 5	Normal					1900 coins 2★ Level-Up Manual
Challenge the Galactic Grunts: Part 6	Normal					2400 coins 2★ Level-Up Manual
Challenge Cyrus: Part 2	Normal	Cyrus Sygna Suit	Darkrai Weakness:			2620 coins 2★ Level-Up Manual
Challenge Cyrus: Part 2	Hard	Cyrus Sygna Suit	Darkrai Weakness:			2,770 coins 2★ Level-Up Manual

Johto: Team Rocket Revival

Unlike other Villain chapters, this chapter serve as a direct sequel to Kanto: Team Rocket Returns and the story is set after Sinnoh: Dreaming in Darkness.

Battles

Name	Difficulty	Trainers			Pokémon			Completion Rewards
Name	Difficulty	Trainers			Left	Middle	Right	Completion Rewards
Challenge Proton: Part 1	Normal	Proton			Zubat Weakness:	Golbat Weakness:	Honchkrow Weakness:	150 coins 2★ Level-Up Manual
Challenge Proton: Part 2	Normal							240 coins 2★ Level-Up Manual
Challenge Proton: Part 3	Normal							450 coins 2★ Level-Up Manual
Challenge Archer: Part 1	Normal	Archer			Beedrill Weakness:	Houndoom Weakness:	Golbat Weakness:	900 coins 2★ Level-Up Manual
Challenge Archer: Part 2	Normal	Petrel	Archer	Ariana	Weezing Weakness:	Houndoom Weakness:	Arbok Weakness:	1400 coins 2★ Level-Up Manual
Challenge Archer: Part 3	Normal							1900 coins 2★ Level-Up Manual
Challenge Archer: Part 4	Normal							2400 coins 2★ Level-Up Manual
Challenge Sygna Suit Giovanni	Normal	Giovanni Sygna Suit			Mega Mewtwo Y Weakness: ↓ Nidoking Weakness:			2620 coins 2★ Level-Up Manual
Challenge Sygna Suit Giovanni	Hard	Giovanni Sygna Suit			Mega Mewtwo Y Weakness: ↓ Nidoking Weakness:			2770 coins 2★ Level-Up Manual

Hoenn: Delta of Land, Sea, and Sky

Battles

Name	Difficulty	Trainers	Pokémon			Completion Rewards
Name	Difficulty	Trainers	Left	Middle	Right	Completion Rewards
Challenge Team Magma: Part 1	Normal	Team Magma Grunt	Numel Weakness:	File:Masters323 m.png Camerupt Weakness:	Numel Weakness:	150 coins 2★ Level-Up Manual
Challenge Team Aqua: Part 1	Normal	Team Aqua Grunt	Carvanha Weakness:	Sharpedo Weakness:	Carvanha Weakness:	240 coins 2★ Level-Up Manual
Challenge Team Magma: Part 2	Normal	Team Magma Grunt	Numel Weakness:	File:Masters323 m.png Camerupt Weakness:	Numel Weakness:	450 coins 2★ Level-Up Manual
Challenge Team Aqua: Part 2	Normal	Team Aqua Grunt	Carvanha Weakness:	Sharpedo Weakness:	Carvanha Weakness:	900 coins 2★ Level-Up Manual
Challenge Team Magma: Part 3	Normal	Team Magma Grunt	Numel Weakness:	File:Masters323 m.png Camerupt Weakness:	Numel Weakness:	1400 coins 2★ Level-Up Manual
Challenge Team Aqua: Part 3	Normal	Team Aqua Grunt	Carvanha Weakness:	Sharpedo Weakness:	Carvanha Weakness:	1900 coins 2★ Level-Up Manual
Challenge Team Magma: Part 4	Normal	Team Magma Grunt	Numel Weakness:	File:Masters323 m.png Camerupt Weakness:	Numel Weakness:	2400 coins 2★ Level-Up Manual
Challenge Courtney and Matt	Normal	Courtney ↓ Matt	Groudon Weakness: ↓ Kyogre Weakness:			2620 coins 2★ Level-Up Manual
Challenge Courtney and Matt	Hard	Courtney ↓ Matt	Groudon Weakness: ↓ Kyogre Weakness:			2770 coins 2★ Level-Up Manual

Team Plasma & Two Heroes

Battles

Name	Difficulty	Trainers	Pokémon			Completion Rewards
Name	Difficulty	Trainers	Left	Middle	Right	Completion Rewards
Challenge the Team Plasma Grunts: Part 1	Normal	Team Plasma Grunt	Muk Weakness:	Drapion Weakness:	Seviper Weakness:	150 coins 2★ Level-Up Manual
Challenge the Team Plasma Grunts: Part 2	Normal					240 coins 2★ Level-Up Manual
Challenge the Team Plasma Grunts: Part 3	Normal					450 coins 2★ Level-Up Manual
Challenge the Team Plasma Grunts: Part 4	Normal					900 coins 2★ Level-Up Manual
Challenge the Shadow Triad: Part 1	Normal	Shadow Triad	Bisharp Weakness:	Bisharp Weakness:	Bisharp Weakness:	1400 coins 2★ Level-Up Manual
Challenge the Shadow Triad: Part 2	Normal					1900 coins 2★ Level-Up Manual
Challenge the Shadow Triad: Part 3	Normal					2400 coins 2★ Level-Up Manual
Challenge Ghetsis	Normal	Ghetsis	Liepard Weakness:	Kyurem Weakness:	Krookodile Weakness:	2620 coins 2★ Level-Up Manual
Challenge Ghetsis	Hard	Ghetsis	Liepard Weakness:	Kyurem Weakness:	Krookodile Weakness:	2770 coins 2★ Level-Up Manual