In the fanfic, it could be that Snape is caught in a political struggle within the wizarding world. Harry, who is on the side of the 'good' political faction, uncovers Snape's involvement in some underhanded schemes for the opposing side. As a result, he has no choice but to get Snape arrested to protect the safety and stability of the wizarding community.
Maybe Harry accidentally frames Weasley for something. It could be due to a misunderstanding, like a spell gone wrong that makes it seem like Weasley was involved in some illegal magic use.
Well, it could be that Alexis was wrongly accused of a crime. Maybe a jealous rival framed Alexis for theft or something. Then the story could follow Alexis's experience in jail, how they try to prove their innocence and find the real culprit.
Well, in a Harry Potter pneumonia fanfic, it could start with Harry being cursed by a new dark spell that gives him pneumonia as a side - effect. As he struggles with the illness, he starts having strange visions. These visions could be related to Voldemort's past or some hidden secrets in Hogwarts. Ginny, being worried about Harry, decides to take matters into her own hands and teams up with Neville to find a way to break the curse and cure the pneumonia. The story could be full of mystery and adventure as they explore the unknown parts of the castle for a cure.
Maybe Harry gets arrested because he's suspected of being involved in a plot to overthrow the current wizarding government. Some powerful wizards, fearing his growing influence and popularity, frame him. In the fanfiction, it could show his struggle to clear his name and expose the real conspirators, all while being locked up and facing interrogations.
One possible plot could be that they discover they are brothers early on in Harry's time at Hogwarts. Snape then has to balance his duties as a teacher and his newfound family connection. He tries to protect Harry in secret from the threats within the school, like Malfoy and his cronies.
One possibility could be that Dumbledore arranges for Harry to live with Snape for protection. Snape, though reluctant at first, gradually discovers Harry's hidden strengths and they form an unlikely bond. Harry might learn more about his mother from Snape, which could lead to a deeper understanding between them.
Perhaps in the fanfic, there is some sort of magic that binds their fates together. Snape might discover this connection and, despite their past differences and his own reserved nature, he decides to propose to Harry as a way to accept this newfound bond. It could also involve Snape trying to make amends for his past actions towards Harry by offering this ultimate commitment.
One possible plot twist could be that Snape is secretly protecting Harry not just because of his connection to Lily, but because he discovers a new prophecy related to Harry that could change the fate of the wizarding world. So, he takes Harry in to keep a closer eye on him and train him in a way Dumbledore couldn't.
One possible plot could be that Snape, out of a sense of guilt or a newfound understanding of Harry's situation, decides to take him in. Snape would have to deal with Harry's grief over his parents and his own complex feelings towards the boy. He might start to teach Harry magic in a more personal and different way than at Hogwarts, leading to a unique bond between them.
The plot could be that Snape discovers he has a deeper connection to Harry. Maybe there was some magic involved in the past that bound them in a way. Snape then starts to take on a more protective role. For instance, he could interfere when Harry is in danger from some dark wizards who are still lurking after the war.