Perhaps in the fanfic, Luna has a nightmare about her past as Nightmare Moon. She wakes up crying because she fears that she could lose control again and turn back into that evil form. This would show her internal struggle with her own identity and the fear of repeating her past mistakes.
First, understand the character well. If you want a pony to cry, you need to know what would break their heart. For example, for Pinkie Pie, it could be something that ruins a party she's been planning for a long time. Then, describe the build - up. Show the events leading to the crying moment. Don't just jump to the crying part right away.
Some mlp crying fanfics focus on the ponies' past traumas. For instance, Rainbow Dash could be crying as she recalls a difficult race in her past where she let her team down. The fanfic author uses the crying as a way to show the pony's growth and how they've overcome or are still dealing with that difficult memory.
Another option is to use search engines. Enter the keywords'mlp twilight crying fanfic' along with any other details you might be interested in, such as a specific plot element like 'Twilight crying over a lost friendship'. This can help narrow down the search results and find the fanfic that suits your taste.
Show the reactions of other characters. If the other ponies in the fanfic see Luna crying, their reactions can enhance the emotional atmosphere. For example, if they are sympathetic and try to comfort her, it shows that Luna is loved, but if they are indifferent, it makes her situation even more pitiful.
One reason could be failure. For example, if she fails in a magic experiment that she has been working hard on, it might lead to her crying as she is often very dedicated to her studies and magic practice.
I haven't read this specific 'mlp fanfic' in detail. But generally, it might be about not showing weakness or sadness. In My Little Pony (mlp) universe, the theme could be related to the characters' growth and how they deal with difficult emotions. Maybe it tells a story of a pony who is trying to be strong in the face of challenges and not let others see their tears.
It could be about a young pony who has lost something dear, like a special friendship or a magical item. But they don't want others to see their sadness, so they keep it to themselves and try to be strong when the sun is out (which could represent the public eye).
One possible reason is that he misses his family or his old home. He has been living with Twilight in Ponyville for a long time, but there might be times when he gets homesick. Additionally, if he fails to prove himself worthy in the eyes of the ponies or other creatures in Ponyville, he could be very disappointed in himself and cry. For instance, if he tries to participate in a competition but doesn't do well, he might feel like he has let everyone down, including himself.