When Volcanion arrived at the Azoth Kingdom, Flamel deduced from witness reports that the Pokémon that had appeared was a Volcanion and relayed this to Kimia. She was later seen walking along with Kimia as the latter questioned Raleigh about what he was up to.
Later, after Alva captured Magearna, Flamel contacted Kimia and informed her that she had found some diagrams by Nikola in Raleigh's room, which had never been seen before. She explained that Alva intended to use the Soul-Heart to activate the hidden mechanisms within the castle, which allowed part of the castle wall to convert into a flying fortress.
At the end of the movie, Bonnie was seen proposing to Flamel on Clemont's behalf.