The discipline would probably change a great deal. McGonagall was known for her strict but fair discipline. Without her, students might start getting away with more mischief. Also, the Gryffindor house would lose its strong guiding figure. The new teacher in charge might not have the same understanding of the Gryffindor values. Academically, her expertise in Transfiguration would be missed. There might be a decline in the quality of Transfiguration teaching.
Well, perhaps it was because of a conflict with a powerful figure. Maybe she had a huge argument with the Headmaster or someone from the Board of Governors. If she strongly opposed a decision that the higher - ups were very much in favor of, it could lead to her dismissal. For instance, if there was a plan to cut down on certain magical subjects that she thought were essential for students' education. And in a fanfic world, there could be some made - up reasons too, like a mysterious prophecy that said her presence at Hogwarts would bring some great danger, so they fired her to avoid it.
In such a fanfic, perhaps Harry discovers some long - hidden, damning secret about Dumbledore. Maybe it's related to Dumbledore's past actions with Grindelwald. Harry, being the honest and justice - seeking person he is, feels compelled to expose this secret, which then leads to Dumbledore being fired from his position at Hogwarts.
I'm not sure if there is a specific fanfic with that exact plot. Fanfiction can cover a wide range of ideas, but this one seems quite unusual. Most fanfics tend to focus on more traditional themes like Harry's adventures at Hogwarts, his relationships with his friends, or the fight against Voldemort. However, in the huge realm of fan - created content, it's possible that something like this exists, but it's not likely to be very popular.
It could be Voldemort or his followers. They might see Dumbledore as a major obstacle in their path to power. So they could manipulate Harry, perhaps through some mind - control magic or by spreading false rumors, to get Dumbledore fired. By removing Dumbledore, they hope to gain more control over Hogwarts and the wizarding world in general.
On the other hand, Harry could be proud of himself for standing up for what he believes in. He may think that he has made Hogwarts a better place by getting rid of a teacher who was not treating students fairly. But at the same time, he might have mixed emotions as Snape was also an important part of the Hogwarts environment for so long.
She might use her magic skills to shield Harry from physical harm. For example, she could cast protective spells like a strong shield charm when Harry is in danger from dark wizards. Also, she may use her authority in Hogwarts to keep him away from those who wish to harm him, like making sure he is not alone in dangerous areas of the school.
There's also 'Snape and McGonagall: A Different Perspective'. This fanfic delves into a more complex relationship between them. It starts with a simple encounter and then builds on their shared experiences at Hogwarts, including their different views on teaching and protecting the students. It's a really engaging read.
McGonagall as a guardian might also involve her protecting Harry from the darker forces in the wizarding world more directly. Instead of just being a teacher, she could be the one to shield him from certain Death Eaters or threats. She could use her Animagus form to secretly follow Harry when he's out of Hogwarts and make sure he's safe.
One possible reason could be that she is under some sort of dark magic influence. Maybe a spell has been cast on her that makes her act out of character and abandon Harry.