In the police station office, Kujan tells Verbal about Marquez's death—he says that there were no drugs on the boat because the Argentinians were selling Marquez to Söze's rival Hungarian gang, so they'd be able to get the dirt on Söze.
According to Kujan's theory, Söze hired Verbal and the others to kill the Argentinian and Hungarian gangsters so that he or they could kill Marquez.
Söze finished them off to tie up loose ends: so they wouldn't be able to rat on him.
But since Keaton's girlfriend was actually Marquez's lawyer, Kujan says that this means that Keaton was really masterminding the whole thing—in reality, Keaton was Keyser Söze.
Kujan says Keaton only left Verbal alive to provide a cover story, but Verbal cries saying it was because Keaton was his friend.
But Kujan says that Keaton was heartless, even killing his own girlfriend, Edie, who was recently found shot to death (something Verbal didn't know).
Kujan claims Keaton must not have really died—Verbal didn't see what ultimately happened, just heard the shots and saw the fire.
Verbal cries saying that Keaton really did lead them into the whole scheme and that Kujan's right.
Kujan says Keyser Söze was just a shield, a spook story Keaton used to cover up his own scheme.
Verbal gets upset and refuses police protection. Since he's already been granted immunity, he's able to leave without Kujan preventing him.