The culprit is actually Magical Moon Chef Gohda, an ambassador from the Moon on behalf of the Lunarians. Naturally, with Gohda's supreme alien technology, which is indistinguishable from magic, it was a piece of cake for Gohda to commit the crimes.
As for the motive, Gohda is a genderless Lunarian construct, sent from the Moon by its population, in order to observe rumours of possible human intentions on setting residence on the moon. First, Gohda was employed as a servant in the Ushiromiya household, taking the image of a childish maid, since the Luanrians figured everyone would trust a young girl. However, since Gohda was unfamiliar with Earth's different gravitational field, as well as it's customs and generally how to move about in a little girl's body, Gohda was quite the clumsy maid. Gohda's only real friend was a hologram-based AI, who due to a error from a clumsy crash on the Earth's surface, was stuck in permanent troll mode.
Gohda continued to observe the Ushiromiya family, waiting for the moment that the human's plans might be revealed. However, Gohda did end up making a single human friend, Shannon, who thought Gohda to just be a pitiful clumsy little girl. Gohda originally used her as a connection to humanity, but eventually grew to like her, since Shannon is a such a nice girl.
The time eventually came that Gohda learned of the human's plans to invade the moon, but by then Gohda had found an obstacle in the original plans to exterminate all humans involved in the plan: Shannon. By then, Shannon had fallen in love with Battler, and out of kindness for Gohda's sole friend on Earth, Gohda decided to wait until Shannon left the island before executing the plans.
Well, we all know that Battler took six long years to return, and when Shannon could no longer bear her withered love for him, she tried to throw them away. Enraged at her pain, Gohda decided to wait until Battler returned, and would only offer him mercy if he could remember the cause of her pain and repent.
So, when Battler returned to Rokkenjima, Gohda abducted him and trapped him in a moon base which resembled the layout of the Meta-world, and viciously and apparently impossibly killed off everyone else on the island, except for Eva who was exploring Kinzo's Bat Cave underneath the Kuwadorian.
It took twelve long years, since Battler is incompetent, but he finally understood what really happened on the island and the reasons for it happening, and repented at Magical Moon Chef Gohda's feet, who, no longer bound to orders, allowed Battler to return to Earth. Of course, beng trapped in a Moon base of highly advanced techonology, Gohda did not allow Battler to age one bit, as to preserve the mental acuity of his mind, and gave him a cloak to protect him from any dangerous elements of the advanced technology.