One interesting plot idea could be Allen and Kanda being forced to team up on a mission in a completely new and dangerous area. Maybe they have to deal with a powerful Akuma that has unique abilities they've never encountered before. This would force them to rely on each other's skills, with Allen's Innocence and Kanda's sword - fighting abilities working in tandem.
A really interesting plot could be that Kanda and Alma get stranded in a strange dimension during a mission. In this dimension, they have to rely on each other more than ever to survive and find their way back. Along the way, they start to understand each other's motives and fears better. For example, Alma's fear of being used again could be explored, and Kanda's loyalty to the Black Order could be put to the test.
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.
One plot idea could be that Allen and Lenalee go on a special mission together in a new, uncharted area. They face strange akuma and have to rely on each other's unique abilities more than ever. For example, Allen's cursed eye and Lenalee's dark boots play crucial roles in fighting off the akuma hordes.
One common theme is the exploration of their pasts. Both Allen and Kanda have troubled pasts that can be delved into in fanfiction. Another theme is their growth as characters, especially in relation to each other. For example, how they overcome their differences and become better comrades.
In D.Gray - Man fanfiction, Allen and Kanda often have a complex relationship. They are comrades in the fight against the Akuma, but their personalities clash. Kanda is hot - tempered and Allen is more gentle and kind - hearted. Their interactions range from bickering to grudging respect for each other's abilities.
One great place to find Kanda x Allen yaoi fanfiction could be Archive of Our Own (AO3). It has a large collection of fan - created works for D Gray - Man. Just search for the tags related to Kanda, Allen, and yaoi.
Maybe the Earl hides Allen in a parallel dimension where time moves differently. Allen has to find a way to get back to his own world while also dealing with the strange rules and creatures in this new dimension. The Earl's motives for doing this could be to keep Allen away from the Order and use his power for his own evil plans later.
A great idea could be that Kanda is hurt in a magical experiment gone wrong in the Black Order. It was an attempt to enhance his anti - Akuma weapon, but something backfires. This would not only physically harm him but also make him question his role and place in the Order. He might start to doubt if all their efforts are really worth it.
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.
Perhaps a story where Marian Cross is framed for a crime within the Order, and Allen is the only one who believes in his innocence. Allen then sets out to prove Marian's innocence, facing many obstacles and enemies within the Order. This could lead to a lot of action and also some deep emotional moments between them as they face this difficult situation together.