The Snake Within (M) by @Felpata_Lupin , an AU story set during Harry's time at Hogwarts. 

This is the sequel to 'All The Truth About Jimmy Portman', set in Harry's second year, following a turbulent first year with a number of revelations (which I am not going to discuss in detail here in case you have yet to read the first story). There are a number of key differences to canon - Harry's parents are alive, and Neville, a Slytherin, is The Boy Who Lived. It's such a captivatingly-written story, full of family dramas, mysterious happenings at school, friendships and rivalries, and there are a couple of romantic subplots as well, featuring Sirius Black and Remus Lupin and their respective partners. 

Due to the disturbances of first year, there's a lot of uncertainty in the air. Poor Harry has a new family and reality to adjust to, and he's finding it difficult to cope with all the changes, all of which were out of his control to begin with. Fortunately, he has a good set of friends to support him through the rough times (if only he would always let them - eh, Harry?). Not only is Harry dealing with his new life, but Neville, who has become friends with Draco Malfoy, is 'hearing things' around the corridors of Hogwarts. Things that a certain Ginny Weasley is completely unaware of her own involvement in...

If you've never read this story, I highly encourage you to delve in!