Blue Eyes is first found on top of the Wireless Tower, where Raikou destroys the communication device that connects Oblivia to the Ranger Union. She is next found in the Old Mansion, to find a book about the history of Oblivia, where she uses a Meganium. After the player captures her Meganium, Ukulele Pichu will then paralyze her, so the player will be able to take her as a hostage. Once being told she can be exchanged for the player's partner inside the Daybreak Ruins, she is then escorted by the player through the Daybreak Ruins. Upon entering the ruins, she notes that the poses Red Eyes and her do is in fact inspired by the poses of Rangers, and asks the player to do one. She says that while she "hates to admit it" she thinks "that looks pretty cool". Very shortly later, after the player rescues some more Pichu, she comments that she wonders "when she will get to be free", hinting that she may not have joined the Pinchers voluntarily or no longer wants to be a part of it. At the end of the ruins, she is swapped for the player's partner only for the player to be tricked into battling an Entei straight afterwards. She is then found in the Submarine, where she uses a Feraligatr. After she is beaten, Purple Eyes exiles her from the position of leader due to her capture and multiple failures and in her anger, she initiates "Plan Z", resulting in the Submarine crashing into the seafloor. Then, on the way out, the player saves her by pulling a box off her. Also, after she is booted out of the Pokémon Pinchers, she spills everything she knows about Red Eyes's plan on Faldera Volcano to the player.
After capturing 300 kinds of Pokémon, two grunts under Blue Eyes' leadership go to Rand's house looking for help. They plead that the player save Blue Eyes after she was trapped underwater by a large boulder during a mission. Once she is retrieved, the player is then pursued by an aggravated Pokémon. Blue Eyes, thinking the Pokémon is after her, flees. Once aboard The Union, the Pokémon that has been following the player emerges and turns out to be Lugia. After Lugia is calmed down, Blue Eyes explains that she was after a piece of treasure she thinks might have belonged to Lugia, which turned out to only a fake of the real Rainbow Grail. Prof. Hastings then explains that it was more likely the pollution making Lugia mad than the Pinchers, much to Blue Eyes' relief and understanding that she hadn't caused its rage.
Some grunts further explain that they were the ones after the treasure and Blue Eyes came to save them. Blue Eyes, unable to swallow her pride, denies the grunts' story, and the platoon is invited on board The Union to watch the sunset. It is then that she and several other people witness the player complete his/her Browser.