One possible scenario could be when Lupin has to leave Hogwarts due to his werewolf secret being revealed more widely. He might cry because he has found a sense of belonging there, with his friends and students. He loves teaching and seeing the young wizards grow, and leaving all that behind is heart - breaking for him.
One interesting fanfiction idea could be that Snape discovers a hidden Horcrux that Lupin unknowingly has in his possession. Harry Potter then has to figure out how to destroy it without harming Lupin. This would add a whole new layer of drama and mystery to the existing lore of the Harry Potter world.
One great fem Harry Potter and Remus Lupin fanfiction is 'A Different Path'. It explores an alternate universe where Harry is female and her relationship with Remus develops in a very interesting way. It delves deep into their characters and how they interact in a world full of magic and mystery.
One possible reason could be his self - loathing due to his werewolf condition. He might think he's not good enough for Tonks and that she'd be better off without him, fearing that his lycanthropy could bring danger or a difficult life to her.
When thinking about his own difficult past as a werewolf. Memories of being ostracized and feared by others could resurface. He might cry as he reflects on all the pain and loneliness he had to endure throughout his life.
There are also authors who are really good at character development in their fanfictions. Take 'TonksTales' for example. They create stories where Lupin and Tonks' characters are very true to the original books but also have new and interesting facets added. They might explore Lupin's insecurities in a new light or show Tonks' Metamorphmagus abilities in unique situations. Another great author could be 'RemusAndNymphadora' who writes stories that are often set in different time periods of the 'Harry Potter' world related to Lupin and Tonks.
One great fanfiction could be about Remus Lupin teaching Harry Potter some advanced defensive magic techniques, with Sirius Black popping in now and then to offer his unique insights. It might explore how Remus's calm and methodical approach contrasts with Sirius's more impulsive nature, all while guiding Harry on his journey to become a better wizard.
In such a fanfiction, perhaps Harry would grow up with a more nurturing and understanding environment. Lupin could teach Harry about the wizarding world in a very different way than the Dursleys. He'd likely introduce Harry to magic earlier and help him better understand his parents' legacy.
Many 'Harry Potter Remus Lupin fanfiction' deal with his sense of isolation. Despite having friends, he often feels alone because of his condition. Writers explore how he overcomes this feeling or succumbs to it. His relationship with the wizarding community at large, whether they accept or reject him due to his lycanthropy, is also a common theme.