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 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.
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.
Perhaps Boruto cries when he realizes he has made a big mistake that has put his friends in danger. He is a character who values his friendships deeply, and the thought of harming his friends would be a huge blow to him. He might also cry when he witnesses the destruction of the Hidden Leaf Village or when someone he cares about gets seriously injured.
One scenario could be Lupin sacrificing himself during a major battle against the Death Eaters. He might use his werewolf form to his advantage, taking on multiple enemies at once but getting fatally injured in the process. His last moments could be spent looking at Harry, seeing the hope for a better future in his eyes.
One possible reason could be remorse. Harry might realize that he misjudged Snape all along. Snape had a complex role, and if Harry discovers the truth about Snape's true loyalties and sacrifices, it could lead to him crying out of guilt for how he treated Snape in the past.
Well, perhaps in a fanfiction, Sasuke could cry for Sakura when he discovers a deep secret she has been hiding. Maybe it's something that makes him understand her on a whole new level, like a hidden pain she has endured all this time for his sake. This newfound understanding could stir such strong emotions in him that he can't hold back his tears.
One possible scenario could be that Harry is exiled due to false accusations of dark magic. Maybe the Ministry of Magic, fearing his power after the defeat of Voldemort, spreads lies about him being a threat. Another could be that he chooses exile to protect his friends from a new, unknown danger that is targeting him specifically.
Perhaps in the fanfiction, Harry Potter's death occurs because he tries to rewrite a powerful magic spell that goes horribly wrong. He was always known for his bravery and willingness to take risks in the original series, so this could be an extension of that. His death would then be a tragic consequence of his own curiosity and desire to push the boundaries of magic.
In another scenario, Harry could expose all of Umbridge's wrongdoings in a very public and embarrassing way. He might use the Marauder's Map to find evidence of her sneaky activities and then present it to the whole school, causing everyone to turn against her and forcing her to leave in disgrace. Harry has a lot of friends who would support him in this, like Hermione and Ron.
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.