The majority of this book is taken up with a plot of conflict -- particularly a veiled and very tense conflict between Laura Fairlie, Marian Halcombe, and Walter Hartright on the one hand, and Sir Percival and Count Fosco on the other. The conflict between the two groups starts out as subtle, unsaid, and indirect, but eventually devolves into direct conflict. The conflict is over the money, person, and rights of the youngest person of the five: Laura Fairlie. Sir Percival marries her specifically for her money, so that he may benefit, and the English wife (an aunt of Laura) of his friend Count Fosco may get some money, too. By isolating Laura and playing on her already weak mind, Percival is able to put Laura into an asylum against her will, and to pass off her disappearance as a death by the elaborate use of the real death of her lookalike (and long-lost illegitimate half-sister) Anne Catherick. Percival is the principal beneficiary, but the mastermind behind all of this is Count Fosco.
There is also a very interesting conflict between Fosco and Marian. Marian is at least Fosco's equal (and, since she and Hartright defeat him, perhaps his superior) in intellect, though she cannot match him in cunning. The two recognize each other as great intelligences, but they are diametrically opposed to each other morally. Nevertheless Fosco conceives a passion for Marian, which is only ever expressed to her in a letter. Marian feels nothing but loathing for the man who was responsible for putting her sister Laura in an asylum and faking her death.
Percival, an illegitimate pretender to his baronetcy, is not only consciously in conflict with his wife's protectors, but with his friend Fosco as well. Percival is not nearly as intelligent as Fosco, and is always wanting to rush in headlong and make mistakes. But even more interesting is Percival's own self-hatred; he knows that he is illegitimate, and, because he is ashamed, is hateful to everyone around him.
Marian, the plainer sister who is also poor while Laura is rich, is the least conflicted main character after the almost simple-minded Laura. She is single-minded in her goodness and devotion to Laura, and her sense of justice never wavers. When she is able to get Walter Hartright to help her in matters which no woman of her time would have been allowed to do, she is truly unstoppable. This kind of integrated and steadfast personality was necessary for the heroic lengths she had to go to to save Laura.
There are more minor conflicts -- with Frederick Fairlie, for example, Laura's absent-minded and invalid uncle, who is so feeble-minded that he cannot recognize Laura when she is presented to him. His character, as well as most of the minor characters, is generally played for a somewhat grim comic effect.