Dialga rules time, and Palkia rules space, they lived in an alternate dimension so they decided to fight within their own reality, which would make it bad for the real world too. Dialga and Palkia appear before Ash and his friends and drag the city into their own world. If they destroy this city, they'll also destroy the whole world.

Source: ANN

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Parent story: Pocket Monsters: Diamond and Pearl
Sequel: Gekijouban Pocket Monsters Diamond & Pearl: Giratina to Sora no Hanataba Shaymin