Princes in the Tower

The Princes in the Tower was the collective name for the two sons of King Edward IV of England and Elizabeth Woodville who were locked up in the Tower of London prior to the planned coronation of the elder brother as Edward V of England. The question of what happened to the two princes was a mystery.

The Doctor, then in his third or fourth incarnation, was contracted to solve the mystery by the 64th century publishers of a range of books called Doctor Who Discovers. Due to years of contractual neglect, the job of actually writing the book — tentatively called Doctor Who Discovers: Historical Mysteries — fell to the Fifth Doctor. He attempted to take Peri Brown and Erimem back to 1485 to investigate the issue, but Peri and Erimem became stranded in 1483 when the TARDIS malfunctioned. After being captured by King Richard III, Peri and Erimem were forced to live in the Tower and impersonate Princes Edward and Richard respectively for almost two years as Richard had moved the real Princes to a safer environment. The trio eventually discovered that in fact there never were princes in the tower, but that Edward and Elizabeth had only had daughters — girls that lived as serving wenches under the names Susan and Judith, with the truth being concealed to protect the kingdom from the chaos that would result if there was no legitimate male heir to the throne. (AUDIO: The Kingmaker)

According to another account, the princes Richard and Edward were kidnapped by an agent of the Council of Eight on the eve of the Battle of Bosworth to prevent them from having an impact on history. They were later rescued by the Eighth Doctor and Trix and taken to the 21st century, where they were adopted by Ernest Fleetward. The Doctor was unable to return them to their home time as they would have been killed by Henry Tudor, victor of Bosworth, something he stated had happened in a universe "somewhere close by" N-Space. (PROSE: Sometime Never...)

In William Shakespeare's play Richard III, Richard was depicted as being responsible for the murder of the Princes. Despite people questioning his motives for killing the boys by Shakespeare's time, Shakespeare was, in the Fifth Doctor's words, "fiction-peddling puppet to the House of Tudor and a lapdog to the court of Queen Elizabeth". Elizabeth was the granddaughter of Henry Tudor, who succeeded Richard following the Battle of Bosworth. By the 20th century, the Doctor claimed Richard III was seen as "nothing but tawdry propaganda". (AUDIO: The Kingmaker)

The mysterious fate of the twelve- and nine-year-old siblings led many to believe that they had been murdered. Consequently, the place of their imprisonment became known as the Bloody Tower. (AUDIO: The Battle of the Tower)

In a parallel universe, the Doctor saved the Princes in the Tower. (AUDIO: A Storm of Angels)

The Tenth Doctor once told Martha Jones that he'd solved the mystery of what happened to the princes twice, in two different versions of history. (PROSE: The Secret of the Stones)

Behind the scenes
It is possible that the above events took place in alternate timelines, as the Eighth Doctor's encounter with the Princes occurred when the Council of Eight had collapsed all of reality into a single timeline that they could control, with the Doctor's actions restoring alternate timelines to the universe at the conclusion of the novel Sometime Never....