After waking up in the Pokémon world, Eternatus creates a realm where any Pokémon that enters will not escape. Many of them stumble upon the portal to the world and find themselves trapped in with no way out, lost and confused in this dreamlike land.
But it's not only regular Pokémon that stumble upon the world, soon enough, Dialga, Palkia, and Giratina, a trio of Legendary Pokémon brothers, stumble across the portal and enter it. However, something seems to go wrong as when they come out of the portal, Dialga and Palkia wake up alone, with no sight of their older brother Giratina.
Determined to find him, the twin brothers decide to set off into this wonderland and find Giratina, no matter how far he is from them. And at first, things start to go well for Dialga and Palkia. They confidently explore the world, help the trapped Pokémon whenever they can, and believe that if they stick together, they'll both be safe from whatever dangers that could possibly be in this world, which makes their bond that they had between them even stronger than it ever was before.
Meanwhile, where Giratina is, he's frantically searching for his younger brothers, worried that something might've happened to them, but he is able to calm down once he finds Xerneas, his friend that has also stumbled in this world. He joins her and helps her tend to the Pokémon that are trapped and lost in the wonderland which also starts out well for them both. Their bond between them grows stronger than it had been when they had already known each other back at home.
But then, they find Yveltal, Xerneas's younger brother, beat up and alone in the forest. Giratina finds out that Eternatus, the one who created this world, was the one who left Yveltal for dead.
Determined to free the Pokémon and angered at the fact that one of his friends got beat up, Giratina sets off to find Eternatus, and get rid of him once and for all. He is able to find him, but he wasn't able to eliminate Eternatus, getting himself killed while fighting him.
Back to Dialga and Palkia, despite their confidence, they are growing more and more worried (specifically Dialga) that they won't be able to find Giratina, as it's been more than a couple of days since they stumbled across the wonderland. However, their confidence is boosted up again once they reach an area in the forest where Giratina's footprints lead to. They're both excited, because this might be their chance to see their brother again. However, what was their excitement quickly turns into horror and grief. Once they reach the center of the forest, they only find Giratina's corpse in the middle of a clearing. But their grief then turns into fear as Eternatus, Giratina's murderer, is still there. They try to make a run for it, but they aren't fast enough to escape him and Dialga and Palkia both get killed. Xerneas eventually finds them all, and she is devastated at the loss of all three of her friends.