Sure, Megumi discovers the truth about Toji being his dad in the manga. It's a crucial plot point that brings about various changes in Megumi's storyline and his relationships with others.
There's a fanfiction called 'Unlikely Allies'. In this story, Kenshin and Megumi are forced to work together on a mission. It's full of action and also some really sweet moments between them as they get to know each other better. As the story progresses, you can see their relationship evolving in a very natural way.
One common theme is the development of their relationship against a backdrop of conflict. Since they are in a world full of danger, they often have to rely on each other, which deepens their bond.
Some smaller, more niche fanfiction communities or forums dedicated to the fandom that Kyo and Megumi belong to might also have some great finds. You can search for relevant forums through search engines and then look for the fanfiction section within those forums.
Well, 'Love in the Shadows' is also quite interesting. It sets the story in a more mysterious and dangerous setting. Kyo and Megumi find themselves in a situation where they have to rely on each other completely. The fanfiction is full of suspense and the development of their relationship is intertwined with the plot twists.
The fanfiction 'Yuji x Megumi: The Unseen Connection' is quite good. It takes a unique approach by exploring a hidden bond between them that is not as obvious in the original work. It makes you look at their relationship in a whole new light.
You can try Archive of Our Own (AO3). It has a vast collection of fanfictions, including many about Yuji x Megumi. The site is well - organized, and you can easily search for the specific pairing you're interested in.
As of the latest chapters I've read, Megumi is still alive in the manga. Usually, such major character deaths are significant plot points and would be well-publicized if they occurred.