The world is under a shadow of confusion and misunderstanding
Dorothea marries Mr. Casaubon; Mr. Lydgate marries Rosamond
The reason Dorothea marries Mr. Casaubon is that she assumes that Mr. Casaubon's scholarly research is a great and noble task, and that her own yearning to participate in some grand work will be satisfied by helping him. Her marriage is a result of a whole slew of misunderstandings: she doesn't understand herself or her own desires and she doesn't understand Mr. Casaubon. The same is true of Lydgate's marriage to Rosamond – they both assume that their marriage will be like a fairy tale, and neither are prepared to deal with the reality of life with each other. They both project fantasies onto the other, without understanding each other's true personality.
The confusion gets worse
Mr. Casaubon's jealousy leads him to make the codicil forbidding Dorothea to marry Will Ladislaw; Will's mother's family is unknown; the distance between Lydgate and Rosamond increases
All of the initial confusion and misunderstandings get worse: The question of Will's background becomes a more pressing question because of his relationship with Mr. Brooke. Mr. Casaubon's lack of understanding of Dorothea's personality leads him to misinterpret her friendship for Will Ladislaw. Meanwhile, Dorothea doesn't recognize the anxieties and insecurities that are making her husband unhappy. Will thinks that Dorothea doesn't like him anymore, and Rosamond's alienation from her husband leads her to develop a crush on Will. Dorothea mistakenly believes that Will and Rosamond are having an affair.
Everything is made clear!
Raffles tells Will about his mother's family; Rosamond explains to Dorothea that Will is innocent and still loves her; Fred learns that Mary Garth has loved him the whole time.
All of the misunderstandings are clarified. Rosamond is not, in fact, having an affair with Will Ladislaw. He and Dorothea finally express their undying love for each other. The mystery of Will's background is finally cleared up. The scandal associated with the death of Raffles is explained away. Lydgate and Rosamond might not live happily ever after, but at least Rosamond doesn't try to initiate any more extramarital affairs.