I got an idea for Scrappy in Mystery Incorporated (you know - to prove he could work in a darker show. However, I have only seen the series in snippits, so expect some distorsions.

I would make him as a foil to Professor Pericles. I don't believe that Pericles is Scooby's counterpart, but he and Scrappy share so much in common. Let's start with the micro. Both are considered pint-sized powerhouses (Pericles knocked Mr. E down with a 360-degree feather-flip and killed Ed Machine with brute force), both have a knack for catchphrases (Pericles starts speaking German bits A LOT in season 2 just because... well, just because), and they act so pretentious about their skills (Scrappy brags about his "puppy power" while Pericles will say he's the smartest bird/parrot criminal ever).

Now with the meta, which would be essential to the story. The first season would have Scrappy as a supporting character (like as a sixth member). For the first few episodes, he's actually beige and true to his scrappy, yet harmless, self. Then, when they find the trail of clues left by Mr. E., the gang would actually be uninterested in this "mystery", but Scrappy would suddenly start to be very focused with it. He insists that the gang must make this top priority, even as far as leaving his assigned duties on minor cases to spend time on the overarching mystery. Then, when the gang collectively gives up and focuses on the mystery, Scrappy's interest turns into borderline obsession. He starts to see Fred, Daphne and Velma as slow, incompetent detectives and tries to get Shaggy and Scooby into his investigation (much to their fright and dismay). Later on, it will be revealed that since Scrappy was not a part of "the Five", he is as much susceptible to the Evil Entity's corruption as the rest of the townspeople. Therefore, it is using Scrappy's aggressive impulsive demeanors as a way to manipulate him into uncovering the pieces of the disk. Nearing the end of season 1, Scrappy basically acts like his 1979-1982 counterpart. During this season, a rivalry starts between Scrappy and professor Pericles (picture Peter Strahm and Mark Hoffman from the Saw movies). Scrappy simply can't get a good read on him, and it infuriates him even more. Remember, Scrappy thinks he can take down men in masks ten times his size. Now this parrot/owl who is as tall as he is is giving him some trouble? At the season 1 finale, it is actually Scrappy who goes to lie down in the car, when Pericles shows up. He taunts him about how he has two pieces and flies away while Scrappy shouts that he will be coming for him, just like in the original take (only Scrappy has taken Scooby's place).

The second season would have Scrappy as a protagonist (or at least as a focus character). Oddly enough, Pericles (the so-called main antagonist) is absent for the first four episodes. I would change that a bit. While the gang are solving their personal problems, a mild cat-and-mouse game between Pericles and Scrappy for a third piece would begin. This would highlight Scrappy's unability to be one step ahead of Pericles. They have a physical confrontation. It's noted that Scrappy acts mad and irrational while Pericles keeps his cool. The owl taunts him some more and eventually has the third piece in his possession. Since the locales are usually dangerous, I would have a certain trap set up for Scrappy, courtesy of Pericles. However, since Pericles sees Scrappy's ignorance and stupidity as "mildly amusing", he leaves him in a half-assed death trap. Scrappy survives, but doesn't realize he was almost killed and is frustrated with himself. At this point in the story, Scrappy's behavior would be noticed by the gang. I'm afraid I can't give you any more details here, as what I have is kinda corny, but suffice to say that the gang knows something is wrong with him. Speed up to the Midnight Zone episode. Scrappy has been benched out due to his erratic behavior, but still follows the gang without them knowing. Somehow, Scrappy knows that Pericles is in the underwater laboratory. He sees an alternate entrance, but for some reason decides not to go in after all. For the first time, Scrappy has decided to back down from a fight. Later on, we find out that he backed down because he thought about his first altercation and wondered if Professor Pericles had meant to kill him (which he wanted to do). In other words, Scrappy was for once afraid of someone. This judgement would prove correct, as Professor Pericles blew up Cassidy Williams and killed her. If he had listened to his Scrappy instincts and charged in, he would have died too. This marks the beginning of an improvement in his character.

Now for meta-element number 1. I know there was an episode where Pericles manipulated Brad and Judy into being in his command and turning their backs on Mr. E, who now has a snake-poison distributor on his body. As this point, we would see Scrappy thinking about Pericles and how dangerous he has become. Eventually, while Pericles stands triumphant over Mr. E., Scrappy utters: "He (Pericles) is not an addition to the gang. He's replacing them". This meta element highlights a major sin of Scrappy's past (with him replacing Fred, Velma and Daphne's roles), but also acts as the beginning of the end for Pericles. Think about this: Pericles used to be the mascot and slightly wise owl. Now he's the mascot with a genius-level IQ and the chessmaster who has everyone else under his command (whether by persuasion or by force). He's the brains, the leader (or manipulator), the mascot and the danger-prone one; Brad, Judy and Mr. E. are reduced as his servants. Now that no one in the previous gang is superior to Pericles, this marks his descent into madness. He thinks no one can stop him now, and his sudden arrogance and letting his guard down is exactly what the Evil Entity needed. He sinks deeper into its corruption: he uses OP strength (reminiscent of Scrappy), he utters German tidbits for no valid reason (reminiscent of Scrappy, minus the German). Basically, while Scrappy gets better, Pericles gets worse.

Ultimately, when the series finale arrives, everyone is reunited near the Evil Entity's sarcophagus. Pericles is about to open it, when Scrappy, now mostly recovered from the corruption, decides to "let himself at" Pericles one last time. They ball in a crack and the soldiers don't shoot for fear of killing Pericles. Pericles screams at Brad and Judy to open the sarcophagus. While the Evil Entity is freed, Pericles and Scrappy have their second and final fight. This time, the roles have changed since their first confrontation. Professor Pericles is totally mad and scrappy, taunting Scrappy with disgust and undisguised contempt, and starts spluttering German catchphrases, reminding him that if he killed Ed Machine (a grown-ass man), he will very well do the same to him. Scrappy remains rather cool, but Pericles's fury is too much to handle. It might look as Pericles will kill him. Then, they get a glimpse of the Evil Entity freeing itself and lunging itself at Scooby-doo. Scrappy sees his uncle on the verge of being possessed. He turns to Pericles and whispers something like this: “I’m sorry for you, Pericles, but I’ll have to let you at em this time”. With that, he throws Pericles into the crack, breaking the wall. Freed, Pericles immediately dashes at the sarcophagus.

Now for meta-element 2. It’s a pretty well-known fact that Scrappy wanting to fight monsters too big for him became quickly tiresome. Some will even say rather cynically that they wished Scooby would give up and let that pint-sized puppy take on the tall human-in-a-costume. That way, the monster could pummel Scrappy and maybe he would stop using confrontation every time. Well, this circles back here in a subverted twist. Well, how does Professor Pericles die in this series? By “letting himself at” the Evil Entity, convinced that he could withstand its powers... and survive. He went from being afraid of the Freak (despite knowing it was Fred’s dad) to being unafraid of acting as a vessel for the most powerful Scooby-doo villain ever. Heck, just before he dies, he realises something is quite not right and that he engaged into an unwinnable confrontation, which ultimately cost him his life. And now Scrappy bore witness to this.

As for the Evil Entity’s defeat, it is noted that Scrappy survives the bloodbath (if he died, all his development would have been undone, and we don’t want that). Once the timeline has been altered, Scrappy, Shaggy and Scooby check out the TV channel and see Professor Pericles, seemingly happy and ... not evil. Scrappy shares his thoughts with Scooby, and wonders if there’s still some “badness” in him, that the Evil Entity only used the bad side of him (corny choice of words, but I couldn’t think of anything else). Finally, Scrappy considers taking a break from mystery-solving and will ponder about his improvement so far. In other words, he stills needs to work on himself. When he feels confident that he’s matured enough, he will come back and join Mystery inc (a good excuse for a send-off). And thus, Scrappy’s story and semi-redemption comes to an end.