One great Harry Potter fanfiction about being alone could be those that focus on a character like Harry during his summers at the Dursleys. They might explore his feelings of isolation and how he copes with it. Maybe he discovers new magic during those alone times.
Some fanfictions might center around Luna Lovegood when she's alone in the Forbidden Forest. Since she has a unique connection to the magical creatures, when she's alone in that forest, she could be having secret interactions with them. These interactions could lead to new understandings of the magical world that she then shares with her friends at Hogwarts.
You can start by looking on popular fanfiction websites such as Archive of Our Own (AO3). It has a large collection of Harry Potter fanfiction, and you can use the search function to look for stories with keywords like 'alone' or 'isolation'.
One great fanfiction could be where Harry feels alone during the Triwizard Tournament. Maybe he's isolated because of the jealousy and suspicion from other students. He might find solace in the Forbidden Forest, encountering some magical creatures that help him see his situation differently.
One interesting story could be about Harry facing challenges alone in the Forbidden Forest. Maybe he discovers a hidden magical creature that no one else knew about and has to figure out how to deal with it on his own.
One popular 'Harry Potter left alone' fanfiction might be those where he has to fend for himself in the Muggle world without any wizarding help. For example, he could be exploring his magic in secret while dealing with the challenges of being an orphan in a non - magical environment.
One example could be a fanfic where Harry uses his cunning to outwit Voldemort in a different way than in the original books. He might use his knowledge of Hogwarts' secret passages in a very clever way to set traps for the Death Eaters. Another could be a story where he manipulates the political situation in the wizarding world by being cunning and making alliances that no one expected.
I don't really encourage the idea of Hermione being tortured in fanfiction. It's a rather dark and disturbing concept. However, if you're looking for well - written Hermione - centric fanfictions that are more positive, there are many that focus on her intelligence and her adventures at Hogwarts without such dark themes.
One great fanfiction could be 'The Slytherin Bond'. In this story, Harry realizes that not all Slytherins are bad and forms a unique friendship with a group of them. They end up working together to solve mysteries within Hogwarts that the other houses are oblivious to.
One possible plotline could be Harry exploring his magical abilities in solitude. He might discover new spells or magical artifacts that he keeps to himself. Another could be him building a secret sanctuary where he can retreat from the wizarding world's chaos.
In some fanfictions, when Harry is alone on the train, he could be transported to an alternate dimension or time. He might meet different versions of his friends or even his parents. This would be a really cool story as he could learn from these encounters and bring back valuable knowledge to his own time and world.
Perhaps the Weasley twins could get into a situation where they're home alone at the Burrow and decide to play some elaborate pranks on any unwanted visitors using both their wizarding skills and some ideas inspired by Home Alone. They could charm objects to move on their own and create illusions to scare off people.