I really like 'The Unspoken Connection'. In this fanfic, the chemistry between Kanda and Allen is palpable. It starts with a simple mission they go on together and gradually builds up their relationship in a very believable way. It's a great read for fans of the pairing.
The popularity lies in their contrasting personalities. Kanda is cold and stoic while Allen is warm and empathetic. This contrast creates a lot of potential for interesting relationship dynamics in fanfiction.
In some fanfics, Allen might be depicted as dead, but it really depends on the specific plot and the author's creativity. Fanfic writers often take liberties with the original story, so there could be various interpretations.
One scenario could be that he sacrifices himself to save his friends from a powerful enemy. Another might be that he succumbs to an illness or a curse that was foreshadowed in the original story but never fully realized. There could also be a situation where he is killed in a battle against an overwhelming foe.
In such a fanfiction, Allen might become a much darker character. He could start to use his powers without any moral restraint. For example, he might not care about innocent bystanders while fighting the Akuma. His relationships with his friends in the Black Order would also be severely strained. They would be shocked and probably try to bring him back to his former self, but it would be a difficult and dangerous process.
The plot could develop with Allen becoming a new antagonist. He starts causing chaos and destruction, and the Black Order has to find a way to stop him. Maybe they try to find a way to restore his humanity, but it's not easy as they also have to deal with other threats in the world of D Gray - Man.
The D'Gray Man manga has indeed finished. It wrapped up with a satisfying ending that tied up most of the plotlines and left a lasting impression on readers.