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Prior to The Escape, Green had managed to come in contact with her long-lost parents, who had since moved to the Sevii Islands after her kidnapping. Green revealed to Silver that she and her parents had planned to reunite with each other on One Island. To celebrate this occasion, Silver had sent Green a new set of clothes for her to wear.
In Now You See Me..., Green arrived at the Seagallop ferry set to head to One Island. While riding, Green was attacked by an invisible Deoxys that easily defeated her Pokémon and used its tentacles to keep her trapped. After the Seagallop arrived at its destination, Green's parents boarded the boat to meet with their daughter. Upon seeing Green, they immediately ran towards her, completely oblivious to the danger she was in. Despite Green's desperate pleas for them to stay away, she was forced to watch as her parents fell into a black hole Deoxys had created. Horrified at what happened to her parents, Green passed out and fell off the Seagallop. After having Poli rescue her, Red and Blue took Green to the Pokémon Network Center to recover.
In Once More into the Unown, Green, Red, Blue, and Mewtwo arrived at the Trainer Tower. There, Green and Blue were fooled by fake images of Green's parents and Professor Oak, allowing them and Red to be caught in a trap. After Mewtwo rescued the three, it pointed out where the real captives were being held. Green's parents and Professor Oak were guarded by R, an artificial intelligence that ran the entire tower. With his Porygon2, Blue managed to temporarily shut down R long enough to rescue his grandfather and Green's parents.
In Meet Deoxys, and Deoxys, and Deoxys, and..., Green, Red, and Blue protected Green's parents and Professor Oak while they faced off against Deoxys's Divide clones. After Ultima managed to break in the area, she lent her Dragonite to Lorelei so she could take Green's parents to safety. Before they left, Green apologized to her parents for having to cut their meeting short again, but promised to return to them after she stopped Team Rocket.
In Epilogue, Green's parents appeared as one of the many people who came to the Battle Frontier as a result of Scott making a wish on Jirachi. Green, who had been freed from the petrifaction by Jirachi's power, became fired up at the thought of her parents watching her battle against the other Pokédex holders at the Battle Dome tournament.