The conflict between Holling and his seventh-grade teacher Mrs. Baker in The Wednesday Wars by Gary Schmidt is largely a figment of Holling Hoodhood's vivid imagination. He is convinced that Mrs. Baker hates him with a fiery passion, but of course we learn quickly that she does not and Holling is imagining things.
Holling realizes this truth, too, but only a little at a time. When Mrs. Baker unexpectedly offers Holling a cream puff, he is stunned and the ice he feels melts a bit. When she does not scold him for accidentally letting her two rats, Sycorax and Caliban, loose when he was cleaning their cage, Holling warms up to Mrs. Baker a bit more. She, too, seems to have had a bit of a realization when she tells Holling that they have been wasting their Wednesdays and they begin to read Shakespeare together.
At one point in their reading, Holling knows things have changed between them. He says,
She looked up at me and almost smiled a real smile. Not a teacher smile. Think of it! Mrs. Baker almost smiling a real smile.
If I had to choose just one thing that seems to have made the most difference in the relationship between Holling and Mrs. Baker it would be when they started to read Shakespeare together. While there may not have been conflicts before this, their shared love of Shakespeare's language and stories certainly melts any real or perceived discord and unites them.
By the end of the story, of course, the two of them have experienced many things which have caused them to work together on things they both care about, and any conflicts in their relationship are long gone.