The Evil Alien Jellyfish Overlord looks like a giant, alien jellyfish and had the ability to eat regular jellyfish and create Jellions in their place. It then tells the newly made Jellions to eat everyone in Bikini Bottom, turn them into Jellion Clones, and take away the real copies. Near the end of the episode, the Overlord somehow ends up in the Krusty Krab (probability flew/swam over there) where it held everyone, even SpongeBob's spatula, captive in pods inside the freezer. When SpongeBob squirted mayonnaise on it, it was melted away along with all the other clones.
The Evil Alien Jellyfish Overlord's weakness is mayonnaise. SpongeBob managed to find this out after the Jellion Clones in the Krusty Krab only ordered Krabby Patties without mayonnaise. Even one little squirt of the condiment will completely destroy any Jellion and Jellion Clone as SpongeBob and Sandy fought through the Krusty Krab using a jug of mayonnaise. The Overlord was eventually defeated after Sandy turned up the thermostat causing a block of mayonnaise (which SpongeBob threw at it but it froze and the block landed on his head) to melt on it. All of the Jellions and Jellion Clones were killed and Bikini Bottom was saved.
Where the Evil Alien Jellyfish Overlord comes from is currently unknown as it was first seen in a cave at Jellyfish Fields.
It may have come from space since it is an alien.
It is also unknown how the Overlord ended up in the freezer of the Krusty Krab or why it went there. It could've swam there.
The Overlord may have stayed in the freezer because it knows mayonnaise, it's weakness, will get frozen.