After the player and their partner defeat Dark Matter, the Tree of Life comes back to earth. A light descends from the Tree of Life and Xerneas appears, informing the others that it is the Tree of Life.
Soon afterwards, Xerneas comes to the player's partner and informs them that they are the reincarnation of Mew, the ancient Pokémon who battled Dark Matter in the past. Xerneas lets the player's partner touch its horn, enabling him to remember its past as Mew. On the hill with the big tree, the partner tells the player this story he had learnt from Xerneas. The partner also reveals that he must leave the world as when he had accepted Dark Matter, the part of it that had come from Mew must disappear along with the Dark Matter. The partner then reveals that Xerneas had let him retell this story to the player before having to depart. At that, the partner ascends into the sky in a ball of light and disappears.
Afterwards, Xerneas lives at the Tree of Life and can evolve Pokémon in the player's team. However, relevant non-player characters will not be able to evolve. Once the player has connected with at least 600 Pokémon, Xerneas will connect with the team after it is spoken to.