At some point, he joined Mystery Incoporated aka Scooby Gang, with Scooby-Doo, Daphne Blake, Fred Jones, Velma Dinkley. In the team, he always paired with Scooby-Doo. He is a cowardly slacker and the long-time best friend and owner of his equally cowardly Great Dane Scooby-Doo. His actions with Scooby-Doo had been renowned as running gag in Scooby-Doo franchise. Like Scooby-Doo, Shaggy is more interested in eating than solving mysteries. He and Scooby are the only characters to appear in all iterations of the franchise.
Here, Daphne revealed to Sam and Dean about the recent information that Scooby has become heir of now-dead Colonel Sanders, which Scooby saved in the past. Sam and Dean join the gang to the will reading venue in Colonel Sanders mansion. Here, Colonel Sanders revealed about US$ 1 million have been divided to Scooby Doo and rest of Colonel Sanders family, but only if they willing to stay one night in his haunted mansion. All is going well, but when the "Phantom" (Ghost Kid' manifestation) appear and began killing Mr. Simple, Sam and Dean realized that the story had been corrupted as they were very familiar with most Scooby Doo episodes. Sam also warned Dean that if it wasn't fixed as soon as possible, all of the Scooby Gang and the Winchesters could all be killed for real.
When Velma started to finding logical explanation about how Mr. Simple being killed. Shaggy is who announced about what kind of ghost that working for killing relatives for inheritance. He also who noticed a shadow that lurking outside and approaching the mansion, which turned out is Castiel.
When meeting Castiel, Shaggy also make a joke upon his name and compared his name with certain Italian Pizza franchise. The joke somewhat make Castiel feeling uneasy, especially in addition when he encountered Scooby for the first time, which he to the point said them both as "A Scruffy Philistine" and "The Talking Dog", respectively.
When Daphne wondered about who was responsible for killing of Mr. Simple, the lights become flicker off. Shaggy also noticed about temeprature drop in the room. When searching about what happened, the "Phantom" appeared, and Shaggy called out its name. When the "Phantom" fleed from the scene by passing through the wall, Shaggy also commented how can the thing such real can walk through the door, which Velma scteptically said it was due some kind of tricks.
He and the Scooby Gang and The Winchesters also checked another rooms. Here, they found Cosgood Creeps had been killed and his body brutally hanged and mutilated. However, strangely, he and the Scooby Gang just acted coldly without fear, simply walking away from the scene, and did their usual searching. Their collective actss making Sam and Dean confused. But Dean can figure out that somehat strange with the Scooby Gang in this world and also the film where they trapped, and he realized it was work of the real Ghost from their world to messed them up.
The Scooby Gang and the Winchesters eventually joining them in their investigation effort. Here, they divide the team into three. Shaggy, Scooby, and Castiel assigned to a group, which Castiel openly disagree and wondering how famed captain that was leading a Castiel's garrison of angel now assigned with "A Scruffy Philistine" and "The Talking Dog". They eventually encounter the "Phantom" in the basement. NAd they eventually running from the "Phantom" in comical door-to-door manner (a running gag in usual Scooby-Doo episodes). They running and running until they eventually corenered in a room. All the Scooby Gang now begin to convinced that they actually encounter a ghost, except Velma that still openly voiced her scepticism. But when, her glasses and all windows pane become extremely frozen and the "Phantom" appear, she later being convinced something went wrong here.
Fred openly attacked the "Phantom", only to be smashed hard enough to a marble bust in other side and get real bleeding and body injury, making him fainted temporarily. The "Phantom" also pinned Velma and Daphne to ceiling. Scooby and Shaggy started to run for saving his life, but only for being levitated and thrown him away to the window. Daphne helplessly calling out Shaggy. Scooby helplessly seeing all his friends in danger, but cannot doing anything. At this critical time, Sam and Dean picked a pair of chandelier, harming the "Phantom" and making him retreat temporarily.
Shaggy, now only hanged with a metal frame in balcony, helplessly shouting for help. The frame suddenly break due to his weight. Scooby jumped for saving his best friend. Scooby can caught Shaggy, but now both of them free falling. Castiel, caught both of them, and somewhat using the "cartoon physics" to make his trenchcoat as makeshift parachute. All of the three safety landed in the fround, but Shaggy hand broken in the process.
Shaggy, now being confused, openly exclaiming that something wrong happening there. He recounted his past experiences of potentially fatal accidents never make him became beaten up or seriously harmed. He also realising that the "cartoon physics" of his world strangely altered, so now he got being harmed. Sam, Dean, and Castiel later revealed that the "Phantom" is real ghost, not the fake ones that the Scooby gang always encountered. Shocked from the revelation, the Scooby Gang started to having mental breakdown. Dean later reminds them about their successes in the past for solving cases. They later managed to work together again to end the "Phantom" problem.
Fred, Shaggy, Scooby, Velma, and Daphne managed to set trap as usually they do, while Sam, Dean, and Castiel devised means for trapping the ghost. After the trap was set, Velma later sent Shaggy, Scooby, and Castiel to act as bait for luring "Phantom". However, the plan went awry when "Phantom" reacted with iron chain that supposedly tripped him, but get burned instead. When "Phantom" suddenly became incorporeal again, all the trap mechanism backfired and hit Shaggy, Scooby, and Castiel. Dean, knowing that Fred trap not working for real ghost, initiating Plan B that involving trapdoor in the house. Together, they lure the "Phantom" into library. Fred, Daphne, and Velma acted as bait in the library, While Shaggy able to distract the "Phantom" enough so Scooby can lay enough weight to the "Phantom" and activate the trapdoor mechanism. The "Phantom" successfully trapped in salt circle trap.
After the "Phantom" revealing himself as The Ghost Kid and his motives. Sam, Dean, and Castiel realized that such revelation is too shocking to Scooby Gang, and will lead them into panic attack, after seeing now overly nervous Scooby Gang started to overthinking about what happened next and they started to wonder desperately about potentially harmful acts. Sam and Dean realized, they cannot being leaved like this. Sam and Dean asked to him to change his shape to Cosgood Creeps, and telling them their usual version of the truth, restoring the original storyline as usually done in Scooby Doo episodes (Greedy people using tricks to drive out other people, so enabling them to possess of large amount of wealth which is not his right). Dean also promised to freed him from Jay enslavement.
After the revelation, Sam, Dean, and Castiel later parted their way with the Scooby Gang. Before his departure, Castiel healed Shaggy broken arm. Castiel then hug Scooby and Shaggy, praising their brave acts in saving each others life. Castiel also jokingly mention about "Danger", which promptly make Shaggy and Scooby running, joining the rest of Scooby Gang for celebration. After the story fixed, the Ghost Kid apport Sam, Dean, and Castiel return to main world, leaving Shaggy and the rest of Scooby Gang in their animation world.
In Mint Condition, Sam uses cleaning supplies inside of a Scooby-Doo themed lunch box, showing pictures of Scooby and Shaggy, to blow up a door. Dean later says that next year they will do Halloween right and even suggests multiple matching costume ideas to Sam, one of which being Scooby and Shaggy.
- Shaggy believes in the Afterlife, and tells Daphne "every freakin' time".