If I would make an episode different, it would be the Season 9 special "SpongeBob, You're Fired".
I would change one scene of the beginning, along with the middle to the end of it.
First, Mr. Krabs would immediately stop SpongeBob from crying, as he explains it would get his customers to leave and Krabs won't let that happen again, because it first happened with her daughter Pearl when she complained about her Acne.
(When it happened: Barnacle Face - Season 8, Episode 164, Segment A)
The rest of the scene then would then be mostly the same, Krabs try to get him out of the Building, he tries to bawl some more, Squidward then slaps him out of it, saying that it can get annoying & distracting. He would then put a cork in his mouth. Then he dollies him out of the building, drops him off and still says: "You know, it just won't be the same around here without you. You'll have to visit sometime..."
Second, Sandy's psychological test food wouldn't be chum-based, with toxic waste thrown in.
Instead, it would be a batch of Brownies, but made mostly of Peanut Butter.
Third, fast forward to the middle of the special, after things not working out at Weenie Hut & Pizza Piehole, the bit-of-messy mishap still happens at Taco Sombrero, but this time, he doesn't fire him. Instead, he gets the customers that tried the "Burrito Burger" cleaned off, then gets him to tweak the thing he made, eventually to be a sandwich made of thick Tortilla "buns" and a few weeks pass, and it becomes the most ordered product on the menu. Because of that rewrite, Patrick would then have have no more involvement whatsoever.
Because the show has no continuity whatsoever, he would have to get his real job back eventually.
By Wednesday, there's a knock at his door, which he then opens. The Hotdog Minions still get SpongeBob in a giant hot dog bun and take him back to Weenie Hut. It turns out Mr. Weiner has given him another chance because his idea "Weenie Patties" is a hit, while forgetting his mentioning of firing him. Until Pizza Pete comes along to kidnap him also. And then the rest is mostly the same, except Wet Noodle's "Noodleman" (Which I'll rename to "Xian Noodsum") isn't involved in the fight. The "Pay Toilet" would also cost a Quarter, not a Nickel.
This is because of Krabs' realization of a Quarter having more value then a Nickel.