I want the games to establish her as a marine researcher, maybe out investigating Navel Rock (retconned into a place more like Seafoam/Whirl) with her close friend and Sevii's local professor,
Philena Ivy (or someone
heavily based on her) and her other close friend and fellow E4 member, Lance (who's always been fascinated by Lugia, a dragon-like Pokémon he heard stories about growing up in Blackthorn).
While there, they run into Archer, Ariana, Petrel, and Proton. They have stolen the Blue, Yellow, and Red Orbs in hopes of awakening Lugia (after placing them together on an altar at the very top of Navel Rock) and sending the ultimate message out to Giovanni (who vanished after disbanding Team Rocket).
The first Orb, the Red One, is at Mt. Ember (retconned into a dark, creepy volcano; Red Orb is roughly where the Ruby was in FRLG). At the end of the tunnel (and several Rocket Grunts) is Proton, who runs off and drops the Red Orb after you defeat him.
Just as you exit Mt. Ember, you run into Ivy, who has just received a Pokégear call from Lance; he's at the Rocket Warehouse on Chrono Island and ran into some trouble getting the Yellow Orb. You head there, beat some more Grunts (including Jessie and James, in their final appearance. More on that later...), and enter a back room to find Lance being cornered by Ariana and Petrel. Ariana mocks him, telling him "However strong you may be, you can't take both of us at the same time. Sorry, baby. Now get ready to be thrashed," and when she sees you barge in, she tells him something along the lines of "What? You had an accomplice? Where is your sense of honor?"
You and Lance fight Ariana and Proton in a tag battle, and after beating them, they run off to Navel Rock (where Lorelei and Archer are), but not before Petrel drops the Yellow Orb. Afterwards, Lance tells you that he had been snooping around and discovered Archer's plans to rebuild Team Rocket in Johto and create an evolution-inducing device; he snapped photos and made copies, planning to investigate this at a later date. He then, expresses concern for Lorelei and takes you back to Navel Rock (via flying on his Dragonite), where she, Archer, and the Blue Orb are located.
When you get there, Lorelei is arguing with Archer (who is implied to be her ex-boyfriend), who mocks her for being a "silly woman who doesn't know better," and she calls him a "selfish pig." In response, Archer slaps her, making her glasses fall to the ground, and Lance runs forward, threatening to unleash wrath on him if he sees him hit her again. Archer evilly laughs, accusing Lorelei of always needing her "boyfriend" to rescue her, and she calmly gets up, puts her glasses back on, and hits him right back. Lorelei tells him that she can rescue herself just fine, and she challenges him to a battle.
Archer dusts himself off and calls Proton over, telling Lorelei that she's going to have to fight the two of them at the same time. Lorelei grabs you and says "No problem." You and Lorelei get into a tag battle against Archer and Proton, after defeated, Archer hands over the Blue Orb and vows that this won't be the end of him or Team Rocket.
Once the Rockets leave, Lorelei tells you about the legend behind the Orbs, and their connection to Articuno/Zapdos/Moltres and Lugia. She says that the birds have been seen roaming Kanto ever since the Orbs went missing, explaining why they were at Seafoam/Power Plant/Victory Road instead of the smaller islands surrounding Navel Rock. She, then, points you in the direction of the altar, and you climb up there, placing the three Orbs together. One amazing cutscene later, you get into a battle with a L70 Lugia, and after you either capture or defeat it, Lorelei and Lance run up to you and express amazement at what they witnessed. They thank you for helping them save the day and return to the Indigo Plateau, unlocking the rematch Elite Four. (They will both have completely different dialog if you return to rebattle them.)
On certain days of the week (after completing the Lugia event), you can find Lorelei and Lance on certain days of the week training together in Navel Rock. They will challenge you to a double battle and after defeating them, Lorelei tells you that she is considering leaving the Elite Four sometime in the future. She feels that being there is limiting her potential as a trainer (which Lance agrees with, as she is seen defeating him as we arrive) and keeping her from her passion for research. We also learn that a new League is being established in the Sevii Islands, and they want Lorelei to head it as its Champion... Which is where she'll be when we revisit her story in the sequel (Gen 2) three years later.
