The princes were murdered by Margaret Beaufort
Margaret Beaufort, the intelligent and calculating mother of Henry Tudor, had the means and motive to carry out the murder of the two princes in order to secure her son the throne.History
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Margaret Beaufort, the mother of Henry Tudor managed her son's support in England and was the driving force behind his attempt to acquire the throne. Margaret was said to be cunning, intelligent, and extremely devoted to her son. After Henry was forced to flee to Brittany due to his involvement in the Battle of Tewksbury, Margaret went to extreme measures to attempt to bring her son back. She had even gone as far as to orchestrate multiple rebellions in order to make it possible for her son to return to England. Margaret’s ambitious nature and her unconditional devotion to her son would have given her the motive and means to murder the two princes. The deaths of the princes would have made it much easier for Henry to ascend to the throne. If either of them had lived and become king, Henry would have more political adversaries than Richard III to remove from the throne. Beyond this, the death of the two boys under Richard's protection garnered more support for Henry's cause as people began to question Richard III's character and his innocence. Margaret could definitely have murdered the princes in order to ensure the safety of her son, and to keep herself and her family in power.
One of the largest cases against Margaret Beaufort being the murderer of the two princes in the tower is her lack of access to the princes. Both boys were locked away in the Tower of London when they disappeared and although some argue that she could have bribed guards to murder the boys, this action would put her and her son at extreme personal risk. Beyond this, Margaret was also known for being extremely pious and murdering two children would seen historically out of character for her. 
Rejecting the premises