I'm honestly a little appalled at how long this became. I couldn't resist trying to squeeze in a happy ending. In order to slot this into the start of Crystalised, this is what happens next:
Lloyd: While he is becoming comfortable with the occasional social visit, he still doesn't feel ready to take on any leadership or ninja duties, which is why he reacts poorly the first time he is asked to help with the vengestone problem.
Kai: Trained up a few senior students to take over the classes at Dareth's Dojo. He started doing this after Jay's fall, and felt they were ready to take over full time shortly after the end of the fic. He then starts up his own dojo out in the sticks somewhere, which is the one we see in the show.
Master Wu: Gets deep into his research, isolating himself in the library, mostly unaware of what the other ninja are up to day to day.
Pixal: I feel so bad for not giving Pixal anything to do in this fic. Her feelings are hard ok? She is still there.
Zane: Zane is still living life emotion free, confident that this is helping him more efficiently perform his duties to his teammates and Ninjago.
Cole: Continues to be the unshakeable rock, the heart of the team doing his best to hold everyone together.
Jay: Well Jay doesn't go to the lighthouse. It isn't feasible. Shortly before the start of crystalised, he decides he is all better and goes off his psych meds cold turkey without telling anyone. This makes him get a bit loopy, and start talking to water again. He is still able to be a ninja, but does struggle to keep up on some of the more athletic missions, preferring ones where he is in a vehicle or mech. The damage to his lungs does improve overtime, but he is left with some scarring and never fully recovers.
And a reminder, if you are interested in art, or author's notes, please check out the version over on AO3.