Tower of London The Tower of London was a prison , fortified royal residence , and UNIT headquarters in London . The Doctor visited it on more than one occasion and across several incarnations managed to be thrown in it as a prisoner . History . The Tower was built in the 11th century , construction starting in the year 1066 , ( PROSE : " Magic of the Angels " ) and contained , among other buildings , the White Tower housing the Armour Museum and the Bloody Tower . One of the entrances to the Tower was called Traitor ' s Gate . ( AUDIO : " The Battle of the Tower " ) The Doctor was imprisoned in the Tower on the ( i . e . , the rack ) . ( AUDIO : " Trail of the White Worm " ) In 1400 , the Archbishop of Canterbury Thomas Arundel threatened to imprison Queen Isabella , the wife of the deposed King Richard II of England , in the Tower . ( AUDIO : " The Doctor ' s Tale " ) Henry VIII once sent the First Doctor to the Tower of London , which was where the Doctor wanted to be , as his TARDIS had also been taken there . ( TV : " Strangers in Space " ) Jane Grey was befriended from 19 to 20 July 1553 by her new lady - in - waiting Rani Chandra , a teenage girl from 2010 , whilst residing in the Tower during her brief reign as Queen . ( TV : " Lost in Time " ) The First Doctor assisted Lady Jane and was present at her execution at the Tower . ( PROSE : " The Nine - Day Queen " ) The Sixth Doctor and Evelyn Smythe were imprisoned there by the order of Queen Mary I in 1555 , who was under the erroneous impression that they were plotting to assassinate her and place her Protestant half - sister Elizabeth on the throne . ( AUDIO : " The Marian Conspiracy " ) On a different occasion , the Doctor shared a cell with Sir Walter Raleigh . ( TV : " The Mind of Evil " ) In 1562 , the War Doctor , Tenth Doctor , and Eleventh Doctor were imprisoned in the Tower by Elizabeth I . The Eleventh Doctor left a message in the Tower , which in the future allowed Clara Oswald to use Captain Jack Harkness ' vortex manipulator to escape the Zygon s and free the Doctor . ( TV : " The Day of the Doctor " ) In 1588 , the Fourth Doctor was imprisoned in the Tower . ( AUDIO : " The Devil ' s Armada " ) In November 1605 , King James I of England jokingly threatened to imprison Vicki Pallister in the Tower . ( PROSE : " The Plotters " ) In March 1616 , Sir Walter Raleigh was released from the Tower and arranged for William Shakespeare to be poisoned . ( PROSE : " The Empire of Glass " ) In December 1648 , the Second Doctor , Polly Wright and Jamie McCrimmon were imprisoned in the Tower on Oliver Cromwell ' s orders . ( PROSE : " The Roundheads " ) The Eleventh Doctor was once imprisoned in the Tower without trial on the personal order of King Charles II . Two days later , a sphere twenty feet across was seen heading away from the tower carrying the Doctor . ( TV : " The Impossible Astronaut " ) The Fifth Doctor would return to a cell there , this time with Nyssa , after falling foul of Sir Isaac Newton in the late 17th century . ( AUDIO : " Summer " ) In summer 1897 , Vastra , Jenny Flint , and Strax were asked to guard the Giant ' s Heart until it could be set into Queen Victoria ' s crown during her Diamond Jubilee . ( PROSE : " The Giant ' s Heart " ) During World War II , Nazi officer Rudolf Hess was imprisoned in the Tower . ( PROSE : " The Domino Effect " ) Barbara Wright visited the Tower when she was thirteen . ( PROSE : " Byzantium ! " ) While exiled to Earth , the Third Doctor once helped the Brigadier track down Hingrad , an alien master of disguise who had a secret base at the Tower Hill tube station . From this base , directly under the Tower , the thief hoped to gain access to the British Crown Jewels . Although a combination of the Doctor , UNIT soldiers and Beefeater s were unable to capture the thief , they did prevent him from stealing the jewels . ( COMIC : " Secret of the Tower " ) Ian Chesterton opined to the First Doctor that Frankenstein ' s House of Horrors at the 1996 Festival of Ghana ( which they mistakenly believed to have been within a human mind ) had more spooks than the Tower of London . ( TV : " The Chase " ) The newly regenerated Eleventh Doctor flew west over the Tower , whilst clinging by his fingers from his TARDIS ' doorway , before climbing back aboard . ( TV : " The Eleventh Hour " ) By 2006 , UNIT headquarters was located beneath the Tower of London . From there , Prime Minister Harriet Jones directed the responses of UNIT and Torchwood to the Sycorax invasion of Earth . ( TV : " The Christmas Invasion " ) The headquarters was still used in 2009 , although UNIT also maintained mobile bases in lorries . ( TV : " The Sontaran Stratagem " ) In an alternative timeline , both the Sixth Doctor and the last surviving Dalek were imprisoned in the Tower from 1903 to 2003 . ( AUDIO : " Jubilee " ) In another alternative timeline , the Eleventh Doctor was imprisoned in the Tower by Holy Roman Emperor Winston Churchill on the perpetual 22 April 2011 . ( TV : " The Wedding of River Song " ) The Tower was graffitied by Monos , alongside other London landmarks . ( COMIC : " Sticks & Stones " ) In , 2012 , before the events that brought him together with his former selves , the Eleventh Doctor said he had been imprisoned in the Tower five or six times . ( PROSE : " Magic of the Angels " ) However , he had been held prisoner in the tower three more times than what he recalled when he made this statement , one of which had not taken place yet from his perspective . At the time , he was unaware two of his past incarnations had forgotten being imprisoned along with this version of himself due to their time streams being out of sync , which the Eleventh Doctor learned about when he experienced these events firsthand and was finally able to retain the memory of them . ( TV : " The Day of the Doctor " ) Later in the first half of the 21st century , Kate Stewart summoned the Eleventh Doctor to the Tower to assist in UNIT ' s study of the newly - activated Shakri cube s . ( TV : " The Power of Three " ) By 2013 , the entire Tower was TARDIS - proofed , preventing TARDISes from landing there . By this point , the Black Archive was now located inside UNIT HQ . ( TV : " The Day of the Doctor " ) In September 2015 , Kate Stewart , Osgood , and Bonnie watched Daniel Claremont ' s speech on global warming from the Tower of London . ( COMIC : " Clara Oswald and the School of Death " ) When the Department controlled Britain around the year 2050 , the Tower of London became Dauntless Prison , a prison for all the aliens that arrived on Earth . When K9 Mark 2 and his friends released the alien prisoners there in 2050 , the Department ' s treatment of the prisoners was leaked to the media and the prison was shut down . ( TV : " Liberation " ) Some time around the 29th century onwards , during the reign of Elizabeth X , the tower or a new facility named after the original tower , was incorporated into " Starship UK " . Its dungeon contained the devices used to torture the star whale beneath the craft into moving . Amy Pond visited the Tower during this period with the Eleventh Doctor . ( TV : " The Beast Below " )