In 1485, Henry Tudor defeated Richard III at the Battle of Bosworth and became King Henry VII. He married the Princes’ sister and, in order to do so, had to reinstated their legitimacy. Because they were no longer illegitimate children in the eyes of the law, his claim to the throne could only be accepted if both Princes were dead. Henry was in exile at the time of the disappearance, but it is possible the brothers survived until 1485 and were then murdered.
Henry VII pardoned James Tyrrell, the confessed killer, for “unspecified crimes” in 1486. It is possible that he had ordered Tyrell to commit the murder and Tyrrell later blamed Richard to cover up what had really occurred.