Prisoners of Time was the 12-issue story made by IDW to celebrate Doctor Who’s 50th anniversary. Released throughout 2013, each of the first eleven parts featured a different Doctor, all leading up to the final, multi-Doctor issue in December.The story was released one issue at a time starting with Part 1, with three volumes each containing four issues being sold alongside. Volume one was released on 28 May 2013, volume two on 24 September and three on 18 December.
The Doctor, Ian, Barbara, and Vicki then travelled to 1868, where they attended a lecture by Thomas Huxley. The four of them travelled into the London Underground to investigate a group of missing students and discovered that the Zarbi had populated themselves in the there. Travelling further into the sewers, they found the Animus, who had reformed itself and had moved to Earth to take revenge on the human race. Ian was able to kill it by driving a train into it. The Doctor and his companions prepared to leave, but the Doctor discovered that his companions were missing; having been pulled out of time by Adam Mitchell.
The Voraxx kidnapped Jamie, and took him aboard a slaver ship in orbit. Following Jamie’s signal, the Doctor and Zoe found the trans-mat that led to the ship and found Jamie. They then awoke some Ice Warriors, who started an uprising. The slaves took over the ship, forcing the slavers to leave. As the trio teleported back to the shop, the Doctor was shocked to find his companions missing, having been captured by Adam Mitchell.
The Doctor, Sarah, Liz and the Brigadier went to the nearby UNIT seabase, along with Agent Paul of the CIA, where the Remoraxian Prime was orchestrating its plot to flood the world. Discovering that the American government authorised the nuclear bombing of Great Britain to stop the threat, the Brigadier persuaded the Remoraxian Prime that the Americans would follow through with the attack, and the Remoraxians left Earth, ending the storms. Sarah, Liz and the Brigadier were then abducted by Adam Mitchell.
The Doctor arrived on Agratis to see the Jewel of Fawton and eat a banquet. However, the Jewel had gone missing, and the Judoon had been called in to reclaim it. The Doctor went with his old friend, Provost Mason Vox, and Curator Frez to find Roget, who was suspected of taking the Jewel, while Leela and K9 distracted the Judoon. In the caverns of the Krytuk Valleys, where the Jewel was first discovered, the group discovered Roget. He had placed the Jewel, which was the hive mind for the native crystalline species, in its original place, and awoke the creatures. With the Jewel back with its rightful owners, the Judoon’s search was called off. While Leela was feasting with the Judoon, Adam Mitchell kidnapped Leela and K9
The Fifth Doctor, not long after his regeneration and before the heartrending confrontation with the Cybermen, arrives on an unknown desolate and dark planet to use a small crack in time (such as the one in Cardiff, Wales where the Torchwood base would be formed) to recharge the TARDIS. Along with companions Tegan, Adric, and Nyssa, they begin scouting the area only to find them under fire.
The Doctor has inadvertently landed them in the middle of a skirmish amid the Sontarans and the Rutans – one of many battles during their centuries-long war. From Rutan capture to the base of the Sontarans, the Doctor finds himself in a quandary – he knows he cannot bring this war to an end, but is there a way he can reduce the unnecessary loss of life? And while he finds himself torn between two warring factions, the unnamed kidnapper watches him from afar for the right moment to strike.
Antarctica is now Antarcopolis, a sprawling metropolitan continent reformed from its icy heritages, with small sanctuaries of natural areas left for the native fauna. As they explore the area, the Doctor and his companions fall under attack from robotic security guards, and he is taken to an asylum as a part of a devious plot by the Master.
But the Master is not alone, and employing elements of the Nestene Consciousness in the form of Auton soldiers, Peri and Frobisher find themselves chased further while they search from the Doctor. Meanwhile, as the Doctor begins to remember the ongoing onslaught by the unnamed kidnapper, a voice from the future provides warning and guidance to an unexpected character, providing a surprising but opportune twist.
After helping Drake Ayelbourne of Altair VII, the wealthiest man in the outer rim of the galaxy, with a robot problem, the Doctor and Rose were confronted by a cloaked figure, who introduced himself as an older Adam Mitchell, who had sworn revenge on the Doctor after his mother had die from a brain illness because he could not use future technology to save her. Teaming up with the Master, the most frequently associated companions of every known incarnation up to his final incarnation, save his concealed wartime incarnation.
However, Adam had a change of heart when the Master attempted to destroy eleven different versions of the TARDISes by overloading them with chronal energies he had stolen across the Doctor’s timelines, also wiping out their respective incarnations. However, the energy would keep on growing out of control until it destroyed the universe and reality altogether.
Not wishing to cause this level of destruction, Adam turned against the Master. The Ninth Doctor saw Adam’s dedication to changing his opinion of him and said to Adam that this was his chance to prove him wrong over his past mistakes. Adam stopped the Master’s attempt at causing a cataclysm by blowing up the console controlling the release of chronal energies, but this act left him right in the fray of the resulting explosion. He died moments after making his sacrifice, forgiven by the incarnation of the Doctor he once disappointed. The Ninth Doctor mourned his death alongside his other incarnations and honoured him as a true companion on his memorial that they erected to remember him by.
After the Doctor and Clara ended a civil war among a race called the Frogmen, Adam Mitchell arrived and kidnapped Clara. Returning to the TARDIS, the Doctor traced all the places in which Adam had kidnapped his other companions, just after the kidnappings took place, where he attempted to gain information from people who were there. Arriving at van Statten’s vault, the Doctor found Adam had taken all alien technology, and found the Time Agent Adam had captured and gained the means to track Adam’s vortex manipulator from him. He got to Adam’s Fortress in Limbo and found all his companions in stasis. Working alongside the Master, Adam then threatened to kill all the Doctor’s companions, saying the Doctor could only save one.
Refusing to kill his old companions, the Doctor instead brought ten of his previous incarnations to Adam’s fortress to save their friends. Under the orders of the Master, Adam released an army of Autons at them, but Frobisher released all of the Doctor’s companions, and they began attacking the Autons. The Master then revealed the Auton attack was a distraction, as he blasted the rest of the chronal energy he had drained into the Doctor’s TARDISes, which would cause all of them to overload: destroying all of them and the Doctors at the same time, and destroying the universe as well. Adam, deciding that he did not want the universe destroyed, fought back against the Master, eventually destroying the computer in an explosion that engulfed him. After the Master escaped, the Doctors forgave Adam’s crimes as he died and buried him outside his time palace, with the inscriptions “Adam Mitchell, A Companion True.”