Yveltal first appears on Revelation Mountain after Nuzleaf tricks the player into unsealing the Luminous Water, which would have posed a threat to it and Nuzleaf's goals. Upon appearing, it unleashes its power and turns the player, partner, Archen, Raikou and Suicune into stone. After the two claim the Luminous Water for themselves, Yveltal announces to the world that it plans to bring an end to all Pokémon, and it turns many of the world's inhabitants to stone.
Yveltal is not seen again until the player's entourage (consisting of the player, their partner, Ampharos, Espurr, Jirachi, and Celebi) reaches the end of the Road to Primeval Forest. As they approach the Tree of Life, Nuzleaf, the three Beheeyem, and Yveltal arrive to stop them. However, all of them (except for the one Beheeyem who returned to his senses earlier) uncharacteristically writhe in pain, suggesting that Yveltal and its minions are being controlled against their will by the true antagonist of the game: Dark Matter.
Regardless, they regain composure and attempt to turn the player's entourage to stone, but they are protected by the player and partner's Harmony Scarves. After this failure, the two parties engage in a massive battle, and Yveltal and its minions are defeated. They start writhing again, but then seem to return to their true selves, confused about their situation. They have little time to make sense of anything before they are quickly warped away by Dark Matter.
The player and partner find Yveltal again inside the Tree of Life, where it is restrained by Dark Matter's power, along with Nuzleaf and the Beheeyem. After they free the latter, the player and partner dispel the darkness around Yveltal, freeing it from Dark Matter's control. Yveltal asks them why they would save it, stating that it must be held responsible for its crimes against the world, despite being controlled while committing them. It is further struck by their honest intent when they ask it to look after Nuzleaf and the Beheeyem, and it disappears with no verbal response.
After the player and partner confront Dark Matter itself, Yveltal arrives with Nuzleaf and the Beheeyem in tow; they all rebel against Dark Matter in an attempt to atone for their crimes. However, Dark Matter retaliates and turns its former pawns to stone. Despite this, when all seems lost, the player hears Yveltal and the others' voices encouraging them to never give up. When Dark Matter is finally destroyed, Yveltal is restored, along with all other Pokémon that had been petrified.
When the player's team reaches Grand Master Rank, they gain access to the Buried Ruins, where Yveltal awaits them on the bottom floor. When they reach it, Yveltal seeks further atonement by connecting with the player's team and giving them the Darkness Looplet, one of the Ancient Treasures.
"I am the one called Yveltal. This is your end. You shall all become energy for us."
"Well played, Nuzleaf. Luminous Water can bring back Pokémon turned into stone. It posed a threat to our ambitions. The time of our reign has come to this world! This planet! This world!"
"Consider this a warning to all Pokémon in this world! I am the one true destroyer! I am an end to Pokémon!"
"Allow me to demonstrate. Now I shall send all Pokémon in this world... to the void! I shall snatch away the energy of all Pokémon!"
"It is already too late for you to possibly escape. No matter where you are in the world... No matter how far you run... I shall hunt you down, you will become nothing! Prepare yourselves for the coming of my wrath! Tremble before the great terror I shall unleash! Feel the unending despair I shall bring to the world!"
"You could have just passed us by and never lifted a finger in our aid. Even if we were being controlled by another... we still bear responsibility of our actions. We have done things which can never be undone, nor forgiven. And yet you would move to save us? You would allow us to live...?"