As the player carries out missions, they learn about rumors where Pokémon were found to have turned into stone. On one such expedition, they discover Latios and Latias's petrified bodies, having crashlanded after turning into stone in mid-air. They also encounter Entei, who believes the player to be somehow responsible. Shortly after, Ampharos leads the Society on an expedition to a volcanic island where Entei lives, to confirm his own suspicions about the rumors. In a battle with Entei, the Partner Scarves suddenly resonate and cause the player and partner to evolve into their final forms (albeit temporarily), allowing them to hold Entei back until Ampharos arrives and declares a truce.
Some time later, written warnings begin appearing around town, declaring that Legendary Pokémon are the ones being targeted and the next victim will be Entei. The Society rushes to intercept the rendezvous, but Entei has already been petrified. Moreover, suspicion has now fallen on Krookodile, a local gangster. The Society splits into two investigative teams: one to research how to reverse the petrification, and one to pursue Krookodile. The player's pursuit team chases Krookodile up Revelation Mountain, meeting up with Nuzleaf in the process, discovering a shimmering lake at the summit protected by a pyramid-shaped barrier. The partner, deciphering ancient runes left nearby to everyone's surprise, reveals that only a human can break the barrier, and the other investigative team reports that the lake's Luminous Water is an antidote for the petrification. Just then, Krookodile shows up, as well as Raikou and Suicune who seek to avenge Entei's defeat. Forced to make a decision, the player breaks the lake's barrier, and Krookodile outs Nuzleaf as the one who paid him to write the warnings. Nuzleaf's demeanor changes, revealing himself to be the one responsible for the petrification incidents. Summoning Yveltal to his side, Nuzleaf turns the player's team, Krookodile.
