In the main story
An Umbreon arrives in Post Town and collapses and all the Post Town residents gather to see the fainted Pokémon. After Umbreon is rescued by the Timburr Brothers, Virizion knows him and tells everyone about Umbreon. After Umbreon recovers slightly the next day, Umbreon explains to the player and their partner about Magnagates and how they are created. Everyone then goes outside and heads to the top of the hill in Post Town and Umbreon then places two Entercards into a box, which then a partial Magnagate opens up. Umbreon explains that it is an incomplete Magnagate and that his partner Espeon holds the other two Entercards. The partial Magnagate closes and then the player and their partner head off to the Crags of Lament to rescue Espeon.
In the Crags of Lament, Purugly and Toxicroak both corner Espeon. Espeon still refuses to give the Entercards, and then both Purugly and Toxicroak check Espeon to suddenly discover that Espeon doesn't have the Entercards. While both Purugly and Toxicroak assume that Espeon has hidden them somewhere, they try to force Espeon to tell them. But then, the player and their partner appear and then step in to protect Espeon. After Purugly and Toxicroak are defeated, they run off. Then, the player, partner, and Espeon all head back to Post Town, where Espeon and Umbreon are reunited again. Then, Swadloon and Leavanny appear; Swadloon gives back the Entercards to Espeon and explains to everyone that Espeon entrusted the Entercards to him, so that they wouldn't fall into Purugly and Toxicroak's hands. A flashback is shown and Espeon says that Swadloon found the Entercards she buried before she gave them to him. Umbreon and Espeon tell them that they need to get things ready before opening a path to the Great Glacier.
A few days later, everyone wanted to go to the Great Glacier, but then Quagsire explains that HAPPI doesn't allow more than six Pokémon to travel during expeditions. Then, during the next day, everyone gathers at the hill of Post Town and then Umbreon and Espeon both put in all four Entercards, which summons a full Magnagate to the Great Glacier. The player, their partner, Virizion, Umbreon, Espeon, and Emolga enter, but at the last minute, Emolga pushes Dunsparce into the Magnagate before it disappears. Emolga stays behind at Post Town. Meanwhile, the team arrive in Telluric Path, a dungeon path created by a Magnagate.
Then, at the crevasse of the Great Glacier, another Magnagate is summoned, which creates beams of light to appear, in which leads to another dungeon path created by a Magnagate, called Glacial Underpass.
A few days after the expedition though the Glacier Palace, Umbreon and Espeon summon another Magnagate for the player and partner to travel to Mt. Kilionea, where Munna is located. The player and their partner arrive in Kilionea Road, a dungeon path also created by a Magnagate.
Before the journey back to the Glacier Palace, Emolga summons a Magnagate successfully, which the player and their partner enter, and leads to a dungeon path called Tyrian Maze, which is created by a Magnagate. Virizion thinks that the activities caused by the Glacier Palace lifting into the sky has caused changes to the appearance of the dungeon, resulting in Tyrian Maze instead of Telluric Path.
After defeating Salamence, Umbreon and Espeon call out to the player and their partner. They explain that they have found a different set of Entercards, which they begin to think that Keldeo made them and was an Entercard user. Upon explaining that the new set of Entercards are used for traveling into the sky, Umbreon and Espeon use the new Entercards to create a Magnagate one last time and they all arrive at the entrance to Glacier Palace - Eastern Spire.
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Discover a Magnagate!
- Main article: Magnagate dungeon
In "Discover a Magnagate!" mode, they can be found by scanning round objects in the real world, leading to a randomized dungeon.