Warning: This article contains major spoilers for the story of Pokemon Sun and Moon. Don’t read on if you haven’t beaten the game yet, and don’t want to be spoiled on the plot details.
In Pokemon Sun and Moon, there are two main factions present in the Alola region. The first is Team Skull, which is your typical troublemaking group of villains. They’re made up of a bunch of young punks with dyed hair and skull t-shirts, and they say things like “yo” and “homie,” and do really awkward hand gestures that they probably think make them look cool. But no one in Alola takes them seriously.
On the other hand, we’ve got the Aether Foundation. Helmed by an influential woman named Lusamine, this organization wants to protect all the Pokemon in the world. If they see a hurt creature, they take it in and nurse it back to health. They’re also scientists who focus on studying the nature of Pokemon in an effort to learn more about them. At a glance, things seem pretty straightforward: Team Skull is the bad guy, and Aether Foundation is the good guy. The truth isn’t that simple.
This is your final spoiler warning: don’t read on if you haven’t beaten the game yet.
The truth is, while the Aether Foundation is dedicated to their cause of saving Pokemon, their leader Lusamine is a little screwed in the head. As she progressed further in her research on the Ultra Beasts, Lusamine grew more and more obsessed with the idea of ‘beauty’ and creating a world where only the beautiful could exist. To that end, she began collecting Pokemon that she deemed beautiful, and kept them in cryo-sleep in the labs. Soon, this obsession spread to her research on the Ultra Beasts. Her son, Gladion, recognized her obsession, and stole a special Pokemon developed by Aether Foundation, Type: Null. This Pokemon was built to fight Ultra Beasts, and it’s suggested that Gladion had run away with Type: Null so that he could fight the Ultra Beasts in case the need ever arose.
Lusamine’s daughter, Lillie, became aware of her mother’s obsession soon after that as well. Lillie decided to run away with the creature Cosmog, as she realized that Cosmog was vital to Aether Foundation’s plan of drawing in the Ultra Beasts from the alternate dimension.
When the player character confronts Lusamine and the Aether Foundation later on in the game, it is revealed that Guzma, the leader of Team Skull, was in cahoots with Lusamine the entire time. However, Guzma doesn’t necessarily share Lusamine’s obsession with beauty. Team Skull’s admin manager Plumeria later tells the player that Guzma had become infatuated with Lusamine, and he started to aid her in her plans, gradually breaking apart from Team Skull. Lusamine herself expresses her disappointment in her children, whom she claims had betrayed her by running off with her property. She tells Lillie that she’s no longer her daughter, and that she’s not beautiful enough to be a part of the world she wants to create. It is also revealed that Lusamine plans to unleash the Ultra Beasts onto Alola as part of her effort to build a world filled only by beautiful creatures.
After the encounter, Lusamine and Guzma are sucked into the alternate dimension. By invoking the power of Alola’s legendary Pokemon, Lillie and the player are able to enter the dimension to rescue the adults. After being defeated in battle, and receiving a scolding from Lillie herself, Lusamine gradually returns to her senses. She is then rushed to the hospital to receive treatment to remove the side effects from her fusion with the Ultra Beasts. At the end of the game, Lillie and Lusamine travel to the Kanto region to find Bill in hopes of discovering a full cure for Lusamine.
At this point, Team Skull is fully dissolved. As for Aether Foundation, the leadership of the organization falls to Wicke, and they continue their efforts to find and protect endangered Pokemon.
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