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 various villainous teams from various regions 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.

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:	Mewtwo Mega Mewtwo Y Weakness:	Lapras Weakness:	2,620 coins ★ Level-Up Manual
Challenge Giovanni: Part 2	Hard	Giovanni	Omastar Weakness:	Mewtwo Mega Mewtwo Y Weakness:	Lapras 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.

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			Mewtwo Mega Mewtwo Y Weakness: ↓ Nidoking Weakness:			2620 coins 2★ Level-Up Manual
Challenge Sygna Suit Giovanni	Hard	Giovanni			Mewtwo 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

Sinnoh: Dreaming in Darkness

Cyrus wakes up in the never-ending darkness with Darkrai surrounding him. Team Galactic Grunts and Commanders are wondering what Darkrai done with Cyrus, however he woke up. He said to Darkrai he will never succumb to its nightmares and gains its power. Saturn ask Cyrus what would he like to do next, he said that he will learn about sync stones and Sygna Suits by certain sync pairs. He also want to live in the never-ending darkness after seeing Darkrai's dream.

At the laboratory, Professor Bellis informs that the International Police have started their investigation on Pasio and Team Rocket isn't the only group active with Team Galactic on the move, too. Barry left to stop Team Galactic, and Lucas and Dawn are going to inform Cynthia about it. The player, Lillie, and Paulo will stay at the Bellis lab.

At the ruins, Cynthia asks Giratina if it find anything that interested it. Lucas and Dawn arrived to Cynthia and ask her that she is checking out the ruins again and Giratina also interested on them. Cynthia says that the Legendary Pokémon seem to have appearing here and she is curious about the authenticity of ruins and what kind of history they have. She says that Giratina interested in the traces of other Pokémon that came here. Dialga appears out of nowhere. Cynthia says that Cyrus may have it as well, since he also has Palkia. Dialga disappeared. Lucas wonder if it was trying to tell something. Cynthia don't think it was Cyrus's, but Lucas and Dawn are not sure about that. Dawn reports that Team Galactic is resuming its operations on Pasio and asks Cynthia to help stop them, she agrees to. A mysterious man spots the cave and enters the Team Galactic hideout disguised as Grunt with Croagunk.

At the Centra City, Trainers are asleep with Brock and Erika have arrived wearing their Sygna Suits. They tried to stop Team Galactic plans. Commanders challenge Brock and Erika and they lost. Barry arrives and also want to stop the organization and they left. Brock and Erika sees Hiker mumbling something about the dark. Later he wakes up and says he didn't remember anything, however he was dreaming and walking in the never-ending darkness. Brock report about the mysterious phenomenon to Cynthia. Seems Cyrus using Darkrai to make everyone have these nightmares. Professor Bellis reported that International Police found Team Galactic's hideout and Barry on his way there, too. 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	Darkrai Weakness:			2620 coins 2★ Level-Up Manual
Challenge Cyrus: Part 2	Hard	Cyrus	Darkrai Weakness:			2,770 coins 2★ Level-Up Manual