One idea could be to explore Plankton's backstory. Maybe he wasn't always so obsessed with the Krabby Patty formula. He could have had a normal life before something happened that made him turn to villainy. Another idea is a story where Plankton teams up with other characters from Bikini Bottom in an unlikely alliance. For example, he could work with Sandy to achieve a common goal that has nothing to do with the Krusty Krab.
One significant archaebacterial group from marine plankton is Thaumarchaeota. They play crucial roles in nitrogen cycling and are abundant in various marine environments.
First, think about the aspect of Plankton you want to focus on. Is it his personality, his relationship with other characters, or his goals? Then, come up with a basic plot. For example, if you want to focus on his relationship with Mr. Krabs, you could start with a scenario where they accidentally find themselves in a situation where they have to work together. Next, start writing the opening scene. Describe the setting, like the inside of the Chum Bucket or Bikini Bottom street. Just let your ideas flow and don't worry too much about grammar at first.
No. The original Spongebob series is all about fun, friendship and adventures in Bikini Bottom. The 'Spongebob real story' is a completely different and often very dark and inappropriate take that has nothing to do with the original positive nature of the show.
The uniqueness of their relationship. Tam and Sheldon are both very different characters. Sheldon is extremely intelligent but socially awkward, while Tam has his own set of qualities. Fanfictions that explore how they interact and complement each other are special. For example, Tam could help Sheldon in social situations that he struggles with, like understanding group dynamics at school.
One great Young Sheldon Tam and Sheldon fanfiction could be one where Tam helps Sheldon with a difficult science project at school. Tam might bring in some unique ideas from his own background that Sheldon hadn't considered. Another could be a story about their friendship growing over shared interests in comic books, despite their different personalities.