From Bulbapedia, the community-driven Pokémon encyclopedia.
The Tree of Life (Japanese: 生命の木 Tree of Life) is a location in Pokémon Super Mystery Dungeon found in the Sea of Wonders, where the player can evolve Pokémon. It hosts energy that is said to be the source of all life in the world, and is therefore the target of Dark Matter.
The Tree of Life is embodied by Xerneas. Following the climax of the game's storyline, the Tree of Life can be visited at any time, where Xerneas will offer to evolve the player, partner, or most evolution-capable Pokémon that the player has connected with, provided that the Pokémon's level is high enough. Additionally, once the player has connected with at least 600 Pokémon, Xerneas will connect with the team after it is spoken to, and will also grant the player the Sky Looplet, one of the Ancient Treasures.
According to Celebi, Dark Matter tried to attack the Tree of Life when it first surfaced a long time prior to the events of Pokémon Super Mystery Dungeon, which would have caused the planet to crash into the sun. However, due to the efforts of Mew and a human, Dark Matter was eventually defeated. Fearing that Dark Matter would return one day, however, two Harmony Scarves were created from the Tree of Life, which are eventually worn by the player and their partner. If the wearers of the scarves are in close proximity to the Tree of Life, they can temporarily evolve to their fully-evolved states and will be unable to be turned to stone.
The withered Tree of Life
During the story of Super Mystery Dungeon, the Tree of Life is possessed by the resurfaced Dark Matter, causing it to wither; by the time the player's team is able to reach it, it is almost completely dead. Dark Matter eventually uproots the tree of life, steadily pulling both the tree and the planet into the sun. Thanks to the combined efforts of multiple Pokémon, including Deoxys, Rayquaza, and Mewtwo, the tree's ascent is significantly slowed down, giving the player and their partner time to reach Dark Matter. After being teleported to the tree by Arceus, they climb the tree in an attempt to stop Dark Matter, passing through Tree of Life: Roots and Tree of Life: Trunk along the way.
Before the player and the partner are able to fully defeat Dark Matter, the Tree of Life appears to finally run out of energy, causing the player and partner to revert to their unevolved states and allowing Dark Matter to regenerate itself. However, the player and partner are able to revitalize the Tree of Life, and to ultimately defeat Dark Matter.
After the player and partner are brought back to Primeval Forest after the fight, they discover that the Tree of Life has returned as well, and additionally is back in its fully flourished state. Xerneas appears from the Tree of Life, thanking them and revealing that it is its embodiment.
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