Snape, being a skilled wizard, could use magic to protect Draco. He might cast protective spells around Draco when he's alone or in vulnerable situations. Maybe he uses a spell that alerts him whenever Draco is in danger, so he can rush to his aid immediately.
Well, perhaps Snape uses his position as a teacher to step in. He could have been observing the situation secretly and when Draco was about to do something harmful to Hermione, Snape intervened with a firm command or some magic spell to stop Draco in his tracks.
Another motive could be related to his complex relationship with Dumbledore. Dumbledore might have asked Snape to look out for Draco, and Snape, being obedient to Dumbledore in many ways, would do so to fulfill his request. Also, Snape might believe that protecting Draco is part of a bigger plan to maintain the balance in the wizarding world.
One reason could be Snape's sense of justice. Despite his often - cold exterior, he might not tolerate Draco's bullying behavior towards Hermione.
Well, perhaps Harry uses his quick thinking and his knowledge of magical creatures. He might step in just in time, using a spell to distract Buckbeak before it can harm Draco. For example, he could use a simple levitation spell to lift a small object and draw Buckbeak's attention away from Draco.
In this fanfiction, Harry might also save Draco by appealing to Lucius' sense of self - preservation or family. He could threaten to expose some of Lucius' secrets or illegal activities if he doesn't let Draco go. Or, if there is some underlying family drama involved, Harry could use that to his advantage. For instance, if there's a feud within the Malfoy family that Harry is aware of, he could manipulate the situation in a way that makes Lucius back off and leave Draco unharmed.
Another possibility is that Snape uses his position as a teacher. He might threaten Lockhart with the consequences of harming a student. Given Snape's intimidating presence and his own power within the school, Lockhart would be afraid to cross him. Snape could also call for other teachers to help, making it clear that he won't let Lockhart get away with any harm to Harry.
Well, it could be that Snape has been secretly observing Ron's erratic behavior towards Hermione. When the situation gets out of hand, he intervenes. He might use his position as a teacher to discipline Ron and in the process, saves Hermione. Snape is a complex character with a lot of power and knowledge, so he could use various means like his occlumency skills to sense the danger Hermione is in and act accordingly.
In many such fanfictions, Sirius might use his magic skills. He could be quicker and more powerful than Lucius in a duel. Maybe he uses a powerful spell to stun Lucius and then whisks Draco away to safety.
In this type of fanfiction, Snape could simply intimidate Vernon. Snape has an air of mystery and a certain power about him. He might show up at Vernon's doorstep, give Vernon a cold stare, and with his reputation as a powerful wizard, Vernon might be too scared to oppose him. Snape could then just take Harry without much resistance from Vernon.
Snape could also punish Draco by deducting house points. Since Draco is in Slytherin, losing house points is a big blow to his pride and to the whole Slytherin house. This would make Draco the target of his housemates' ire, adding to the punishment's severity.