He might be in pain because of a potion gone wrong. If he's experimenting with potions in a fanfic, and something goes awry, it could cause him internal pain and distress, leading to tears. For example, a wrongly brewed potion might attack his nervous system.
One scenario could be that he's under the Cruciatus Curse. This curse inflicts intense pain, and Harry has faced it before. In a fanfic, it could be used by a new dark wizard adversary, making Harry cry out in agony.
Maybe he's been injured in a battle against dark wizards. In the wizarding world, battles are dangerous, and getting cursed or physically hurt can cause great pain, leading to him crying.
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 possible scenario could be that the magical characters find themselves on a Muggle plane due to some strange magical accident. Maybe they were trying to apparate but got misdirected into the plane. Then, when the plane starts to crash, they use their magic to try and save the day, like Harry using a spell to slow down the fall or Hermione creating some sort of magical shield to protect the passengers.
In a more complex scenario, Bellatrix could be trying to use a dark magic ritual that would cause great harm to the wizarding world. Harry discovers her plan and has to engage her in a magical struggle. In the process, he manages to turn her own dark magic against her, which results in her death. This would show Harry's ingenuity and his ability to use the enemy's own weapons against them.
In a 'Harry Potter betrayed fanfic', perhaps Hermione turns against Harry. It could be because she disagrees with Harry's more dangerous and reckless plans to fight Voldemort. She might think he's endangering too many lives without proper thought, and this leads to a rift and a sense of betrayal.
In the 'Harry Potter Controls the Elements Fanfic', perhaps Harry discovers his element - controlling powers gradually. He first starts with something simple like controlling the wind to cool himself on a hot day at Hogwarts. Then, as he grows more powerful, he can combine elements. He could create a storm by mixing air and water elements, which he uses to protect his friends from a group of Death Eaters.
Perhaps there's a potion accident. Harry might have been experimenting with a new potion in Potions class, and something went wrong. The potion could have affected his body functions, resulting in his need to wear diapers. It could add an interesting and comical twist to the story.
In some fanfictions, Harry might use a flask to store potions. For example, he could carry a flask of Felix Felicis, the luck potion, with him during a dangerous mission at Hogwarts. This would give him an edge in tricky situations.
One scenario could be that Harry stumbles upon an old wizarding order that was known for their sword - fighting skills. He then gets trained by the remaining members or discovers their old tomes about sword magic. Another could be that in a parallel magical world within the fanfic, swords are the main form of defense against a new type of dark creature, and Harry has to quickly learn about swords to protect himself and others.
It could be when they find out some bad news about the war against Voldemort. Like if they learn of a major defeat of the Order of the Phoenix. Hermione, being highly empathetic and feeling the weight of the situation, breaks down on Harry's shoulder as he is the symbol of hope in their fight and she needs that connection to keep going.