This ask is something I really like, so I've put it up my queue of asks (there are more than thirty of those in my inbox, holy trolls!).
So, in this AU Kanjigar manages to escape during his battle with Bular, so Jim and Toby pass through the canals as usual, with nothing happening. Toby sees that his bro is slightly disappointed that it's just a regular day and suggests investigating the stone monsters Eli mentioned. Obviously, Toby doesn't believe in any supernatural creatures, thinking those are just another one of Eli's delusions, but he thinks Jim needs some fun (and a minor adventure is better than no adventure at all).
It turns out to be a horrible mistake as Bular is pissed because of his failure and is actively looking for a consolation snack. Jim and Toby look like a wonderful meal for him. Bular nearly catches Toby - and it's when Jim awakes his shadow magic, firstly blasting and injuring Bular and then teleporting Toby and himself to the safe location. Jim collapses afterward as he has pushed past his limits.
The next morning, Toby is excited, but Jim is conflicted as he isn't sure it's the kind of adventure he wants. Besides, his newfound magic keeps acting on its own, complicating his life.
Jim comes to Strickler to talk about his issue, but chickens at the last second and tells some lie. Strickler initially believes that it's something trivial, but later notices Jim falling through the shadow portal, and everything clicks. After all, last night, Bular came back enraged, cursing some fleshbag wizard who injured him and swearing to kill that bastard. Strickler deduces that the wizard in question could be Jim. Unlike Bular, he wonders if he can use Jim's talent (after all, all the changelings are connected to shadow magic) and decides to get even closer to his student.
Meanwhile, Douxie visits Jim (as he learned about him from Archie who witnessed the encounter with Bular). Douxie wouldn't get involved in most cases, but apparently, Jim's magic is too strong for someone born during this age, and Jim lacks control, which could easily lead to a lot of damage. So Douxie decides to teach him a bit.
Because Bular has a personal vendetta against Jim, soon enough Kanjigar contacts him as well. Jim learns about the Trollhunter and his mission and proposes to help him (after some initial shock, Jim starts to wonder if there is some meaning to the fact that he got magic). Kanjigar is against it - he has worked alone since the very beginning, and well, Jim is a kid. Jim and Toby still sneak to the Trollmarket, and meet Blinky and Aaarrrgghh there. Blinky believes that having a trollhunting team might not be such a bad idea, so now there are four of them trying to help Kanjigar. Draal eventually joins too, becoming the fifth member. Jim keeps this fact from Douxie because Douxie forbids him to risk his life needlessly (out of concern that there might be another spike in Jim's developing magic which can be harmful to his soul). As for Toby, he gets his Warhammer early on.
Meanwhile, Strickler gets close to Barbara, wondering if she knows her son's secret. He discovers rather fast that she is in the dark about everything and uses it for his own profit.
Much like in the canon, Jim is in the school play, but he skips less because his outings are more controlled (be it magic lessons with Douxie or visits to the Trollmarket), so he has less friction with Claire. Claire still senses that Jim hides something and tries to talk to him about it.
Jim and Toby are the ones who discover the hideout at the museum and basically trigger all the changeling-related events, including Enrique's kidnapping. Enrique is picked because Jim is a regular guest at Claire's house by this point, and Strickler feels that he can use another pair of eyes.
Jim is the one who goes to the concert with Claire in this AU, while Toby babysits Enrique. Claire is initially upset with Jim afterward as she thinks that Toby and Jim decided to prank her together, but after giving it some thought, tries to investigate what is wrong.
Jim still gets Grit-shaka from Draal and ends up exposing his connection to trolls before Douxie before running to fight Bular. Much like in the canon, Bular exposes Strickler.
Claire catches her fake brother herself and encounters Jim, asking if he knows too. Jim decides to tell her everything.
Kanjigar decides to face Bular head-on together with his team (plus Douxie, who joins at the last second). Together they slay him and recover the Killahead.
Now that everything is more or less safe, Claire comes to Kanjigar and asks him to save her brother. Jim and Toby join her pleas, and Jim says that he'll travel to the Darklands himself if Kanjigar disagrees. Kanjigar agrees after some consideration (the previous Trollhunters are against it, but Kanjigar reminds them that his team has slain Bular).
Strickler frees Angor Rot, much like in the canon. Angor, however, disobeys the first command to attack the Trollhunter and judge his skill and goes for Jim instead (he senses his shadow magic and decides to get rid of someone who can possibly become a second Morgana). In this fight, Jim manages to wrestle out the shadow staff. After some examination, Douxie allows him to use it - as the shadow staff, apparently, stabilizes Jim's rather chaotic magic.
The Trollhunters recover the first triumbric stone, but during the quest at the Quagawumps' swamp, the tragedy happens - Kanjigar dies, taking the hit from Angor meant for Claire (it's something that will haunt her for a while). The amulet chooses her as the next champion, but she is conflicted wondering if she can be a good one. After all, she couldn't protect her brother, and Kanjigar died because of her. Draal also doesn't help as he questions her worth (he isn't as bad as he was with Jim in the canon, but his words are still mean).
Jim, however, believes in Claire and says that she can be the best (after all, she is a quick learner, brave, and loyal). Claire starts training, hoping to be able to catch up quickly. Draal warms up eventually and comes to help her.
Angor doesn't make any deal with the Trollhunters in this AU, as he doesn't trust Jim by default. Douxie is the one who suggests stealing Inferna Copula from Strickler, but much like in the canon it ends destroyed, and Angor unleashes his anger at Strickler, Jim, and everyone else. Barbara walks in amid the fight and gets wounded. In this AU she learns everything without losing her memories. Obviously, she is mad at Strickler for using her to get to Jim.
Angor Rot is the first Claire's major opponent, but she manages to defeat him with the help of Jim, Toby, and Draal. Draal feels that his father is avenged and thanks Claire.
However, for Claire, it's not enough. She doesn't want to lose another team member, so goes to the Darklands alone (besides, she was the one who requested that mission to start with). She saves Enrique but ends up trapped.
And here's the problem - only the Trollhunter can open the portal to the Darklands. Jim tries to find an alternative solution and finds a book in Douxie's library about summoning spirits and letting them possess the body. There is a risk, however, as the one who performs it is more vulnerable to possession later, but Jim is willing to risk. He summons Kanjigar's spirit and the team heads into the Darklands to save Claire.
Gunmar getting out isn't the only consequence of that venture. Morgana senses Jim's mind's vulnerability and starts to take over. She resurrects Angor first, then contacts Gunmar.
No one realizes that something is off with Jim at first, chalking most of the stuff to the shadow magic acting up. Claire gets suspicious first and goes to Douxie, demanding if all of that is actually shadow magic. Douxie admits that his fellow student Morgana was odd at times too. After hearing that, Claire is even more worried, and she and Douxie encounter Jim - only to realize that Morgana already fully possesses him.
Claire and Douxie restrain possessed Jim and decide to travel inside his mind to free him. They also bring Toby and Barbara with them, as more meaningful people should make it more likely to succeed. Jim is free, and fighting Morgana gives him a better understanding of his own magic.
With Gunmar and Morgana around the team decides to wake up Merlin (per Douxie's suggestion). And, well, Merlin isn't excited to learn that Douxie got involved and even took a shadowmancer as an apprentice (he is pretty much convinced that Jim will end the same as Morgana if not worse).
Merlin also plans to turn Claire into a half-troll, but as Douxie is around, he investigates the ingredients and discovers what they might do. The team encounters Merlin, and he admits his intentions but tells everyone there is no other choice. Strickler, however, intervenes and makes a guess that there might be some alternative in the Janus Order's records, which turns out to be true. The alternative just requires some blood from a shadowmancer, which Jim gladly provides. Claire becomes a shapeshifter with the ability to change forms at will.
However, Merlin also comes to Jim regarding Morgana. It's possible to seal her inside the Shadow Realm, but all the links between it and the outside world should be cut, meaning that Jim should stay inside the Shadow Realm for good. Merlin appeals to Jim's insecurities and reminds him that the shadow magic is evil, convincing Jim that it'll be better for everyone.
However, Claire overhears this conversation and confronts Jim about it. She also reminds him that Merlin's solutions have already proved to be not the only answer and that their team has already found an alternative once, so it's possible to find another one.
The encouragement from Claire prompts Jim to craft his own spell for the first time to use against Morgana. So, once the Eternal Night comes, both Claire and Jim defeat Gunmar and Morgana respectfully.