These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Moment of Heartwarming: Several examples, such as Gwen and Trent coming to terms with each other, Duncan properly apologizing to Courtney to cheer her up when she came to Lyoko for the first time, followed by Alejandro offering Heather a second chance.
Aelita taking the Lyoko gang to a carnival before the climactic battle with XANA.
Elimination Houdini: Lindsay twice, thanks to Chris's usual way of handling the show and a return to the past. Though in this case, given that Lindsay was the only Team Victory member who wasn't a Lyoko Warrior, it turns out to be a good thing.
Fan-Preferred Couple: The author does ship Courtney and Duncan in the story, but as shown in Lord Maximus's previous story Don't you Care Anymore, he is being careful in untangling the red string that bound Gwen and Duncan, is well-aware of the issues of the Duncney relationship and doesn't jump to anything too soon... which is more than what could be said for how the three are usually handled in fanfics.
Also the time when Gwen was infected with XANA's virus. The results were... decidedly unpleasant.
Blade's true form.
Tear Jerker: Alejandro's backstory; Duncan's counts as well. There's also how Franz Hopper's Heroic Sacrifice turned out to be fruitless and how Aelita's friends were taken away from her.
The Woobie: The "Deal With the Devil" arc is when the story goes deeper into Darker and Edgier territory, where XANA makes almost every contestant go through their worst memories in a simulation bubble. Alejandro, Duncan, Courtney, and Sierra are given some particularly heavy material.