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The Takeover of Ransei is the main story of the game.
Miharu and Oichi have obtained every kingdom in Ransei and after Miharu has obtained the Legendary Pokémon, Arceus, he has decided to return them to their rightful owners.
One day in Chrysalia, while Yoshimoto is playing Kemari with his Forretress, he is attacked by NovaPen and Suchi, who send out their Pokémon, Haxorus and Walrein. They defeat Yoshimoto and force him to give up Chrysalia and leave Ransei. He does so.
Miharu and Oichi find out about this and they realise that NovaPen and Suchi have opened a portal to the Han Dynasty and have acquired Ma Chao and Pang De, warriors from Xi Liang and Mitsunari and Kiyomasa, warriors from Ignis. They find out there are still more and find Meng Huo and Zhu Rong from Nanman. They agree to join.
The other kingdoms have slowly found out about this and are slowly building their army. While training, some Warlords acquire more warriors from the Han Dynasty. NovaPen and Suchi firstly attacks Kenshin and Shingen, from Illusio and Terrera respectively. They are both defeated and decide to surrender, in hopes of sharing the glory with them.
Yoshihiro, a veteran, decides to attack their kingdom, Chrysalia. Big mistake. NovaPen and Suchi successfully defends their kingdom and successfully attacks Yoshihiro's territory of Pugillis. Yoshihiro escapes and joins Miharu's army.
Ginchiyo is suddenly defeated by Hideyoshi, who wants to claim Ransei. Miharu successfully attacks Hideyoshi's kingdom of Violight, forcing them to retreat to Ignis. NovaPen and Suchi notice this, and order Kenshin, Kanetsugu and Aya to attack Ignis and Shingen, Yukimura and Kiyomasa to attack Violight. They all succeed in doing this and Miharu decides to form an alliance with Motochika, Motonari and Nobunaga in the north.
Kenshin wants to attack Cragspur and Shingen wants to attack Avia so NovaPen allows them to, while the others attack Yaksha and Viperia. Shingen and Kenshin are confused. Suchi informs them that Hideyoshi and his warriors have joined as well as Sima Yi, Sima Shi, Sima Zhao and Wang Yuanji. They all successfully assault each area in 4 months.
Ujiyasu, Xiahou Dun, Nene, Hanzo and Kotaro join NovaPen and Suchi. You now can attack Spectra. After defeating No, Masamune and Magoichi join due to Masamune trying to look better than Xiahou Dun.
NovaPen and Suchi are attacked by Motochika and Motonari, who are trying to help Miharu defeat them. NovaPen and Suchi successfully defend and defeats both of them, leaving Miharu isolated. NovaPen insists on Motochika and Motonari to join them, along with their troops. They ask why should they. NovaPen and Suchi inform them that they are from the future and are here in order for peace to happen in the future. NovaPen tells them that Miharu made bad decisions that resurrected Orochi from his grave. Orochi hired Zuo Ci and Nezha and assaulted their time.
Motochika and Motonari are shocked and decide to join. NovaPen and Suchi defeat Nobunaga and Mitsuhide, forcing their forces to surrender, except for Nobunaga. Ieyasu learns of why NovaPen and Suchi are doing this and surrenders. Tadakatsu and Lu Bu are lost for words and walk away from them.
Miharu and Oichi are finally defeated and surrender. A shockwave occurs and a piece of Dragnor has broken apart. Orochi, Zuo Ci and Nezha come out of a portal and this is the final battle. Orochi has with him a Landorus, while Zuo Ci and Nezha have a Celebi and Genesect. Tadakatsu and Lu Bu join NovaPen and Suchi's army for the final battle with Lu Bu hoping to defeat Nezha once and for all.
Nobunaga joins Orochi in battle and Ranmaru and No defect. Keiji appears and asks to train every warrior. If accepted, the Pokémon will have a 100% link and Keiji will give Warriors their respective Legendary Pokémon for the fight.
There are two endings for this game, the Good ending and Bad ending. In the Good ending, Orochi is defeated and they all go back to their respective times. In the Bad ending, NovaPen and Suchi are defeated and Orochi enslaves the human race. In the Hidden ending, by defeating Orochi with NovaPen or Suchi's Latios or Palkia, Yoshimoto will appear in a new mask and armor and wants to battle.