If you dig deep into games such as Paper Mario and it's companions in the series, you notice a few things. One of the most noticeable characters throughout the series happens to be Mario's younger brother Luigi. With some thinking, I managed to realize that the entirety of the Paper Mario series could've been Luigi's own coma dream. These are my findings.
Paper Mario for the N64.
My speculation for this game is that while he was still in the coma, he heard doctors talking about how his family had been going on vacations, or "adventures", without him being there, including his big brother Mario. This causes him to think about Mario going on a fanciful adventure, leaving him at home and excluding him from these activities. Whenever the green-clad plumber is sitting on a rock it's a way of showing he wants his brother back with him; that he wants to get up and go on "adventures" with his siblings. Luigi's notebook/journal/diary entries are based off fantasies he'd had as a kid; he's only around ten-years-old whenever he dreams about the first Paper Mario game.
Paper Mario: The Thousand Year Door (PM: TTYD)
Luigi overhears once again that his family have been doing fine and going on "adventures" without him, this time when he's thirteen years old (Honestly, I don't think the thought crossed their mind to pull the plug on him already). He then dreams of his brother going to somewhere less pleasing, having to save his girlfriend (which he met before he fell into the coma) from some evil force with a ragtag group of misfits as his partners. Luigi subconsciously let himself have his own adventure this time, thinking about his old "friends" and recreating them as partners for his own needs. Blooey is based off some kid he conned money out of, leaving the guys broke. Jerry is based off an older friend who, obviously, hates crossdressing and was constantly nagging him never to do it. Torque was made off of a mechanic he had met, and one of said mechanic's job was ruined by his clumsiness. Screamy was a shy kid at school who he attempted to befriend.
Super Paper Mario
This whole section may sound farfetched and kinda creepy. Prepare for the results of pondering this at 3:00 AM.
There are two possible theories I came up with, but I'll give you the second one because it made more sense.
Super Paper Mario is by far the darkest game in the series, and Luigi dreams of it when he is 16 years old. It's about him thinking about facing his childhood fears that he never got to get over out of the coma. Count Bleck is the fear of vampires almost all of us had at some point, Mimi is the fear of spiders, O'Chunks the the fear of getting beat up or bullied. and Dimentio is a fear of demonic clowns. Nastasia's existence will be revealed later. He hears that Mario has gotten a job as a programmer by a family member that sat by and talked to him. The relative then said something around the lines of "he can make and delete technological worlds as he pleases." This caused him to remember what his ultra-religious mother had said to him about the rapture, or the apocalypse as he remembered it. Along with memories of Christian religion came memories of doomsday cultists, which he portrayed Bleck and his gang as.
Now, what I've been dying to say something about: Mr. L. During the dream, Luigi "realized" that he had been better than Mario in his dreams ll this time, that the villain's side was the winner's side. This, of course, was due to the drugs they were giving him at the time. Luigi dreamed up Nastasia as an excuse for Mr. L's existence, and the reason he works with Bleck's gang in reality is due to Mr. L being Luigi's "opposite" inferiority complex. That pretty much means Luigi's fears would be Mr. L's idea of comfort, but one thing still lingered: the fear of both death and demonic jesters. The fear of death came from when he heard doctors discussing whether to "pull the plug" on Luigi or not, and the fear of demonic clowns/jesters happened when he was really young and went to a haunted house via dare. The dark twist in the game (coughchaptersixcough) was when he heard his own family out there discussing "pulling the plug", the real Mario, his mom, his dad, all of them. His mental state fell into depression, and Mr. L getting murdered by Dimentio was both to experience death and to get rid of Mr. L's existence due the the medication creating him wearing off. The Brobots were Mr. L's replacement for Mario, due to Luigi partially losing all hope in him. Super Dimentio was Luigi feeling as if he was being used, and his realization he was in a coma driving him insane. The love triangle was based off Shakespeare he had attempted to read.
Paper Mario Sticker Star
Sticker Star was a way for Luigi's mind to recover from the trauma that was Super Paper Mario; he was 18 when he dreamed of this one. The game was so lighthearted and happy in comparison to the last installment due to it being a way for Luigi to try to forget what had happened. Luigi looked much paler in this game, probably being a result of newly-attracted Post Traumatic Stress Disorder. I don't know much about SS other than it's happy tone, so for now this is all I have. Hope you enjoyed.