The TARDIS has recently been on the fritz, but now it has gone completely out of control. And the Doctor is nowhere to be found! Meanwhile, white holes have been forming throughout time and space, sucking in everything around them. What does the Hypothetical Gentleman have to do with it all?
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- Priyan says that the Doctor has rejected his name and stands against the Time Lords with the Moment.
- The Doctor mentions Omega, Rassilon, the Valeyard, and the Master as enemies that could return as virtual memories locked inside the Matrix.
- The TARDIS has a LEGO room. It's internal structure is created by turning energy into matter.
- The Sky Jack was sent to drop a third atomic bomb on Kyoto, Japan in World War II. This is historically inaccurate as, while Kyoto was at one point a target, it was removed from the list due to its cultural importance.
- The Doctor traps the Matrix in a toroidal singularity, an oroborus configuration.
- The story features a number of similarities to Journey to the Centre of the TARDIS, including several views of the interior of the TARDIS (including a library), and a scene in which Clara unwisely presses a red button after ruminating over whether it's a bad idea to do so or not.
- At the time of Clara's debut in the IDW series, she had yet to debut in the Doctor Who Magazine comic strip, marking the first time a current TV companion has appeared in an American comic before DWM has featured the character.
- The references to the Doctor rejecting his name and the Moment appear to be prescient on the part of IDW as the comic would have been written and illustrated months before the revelation of the War Doctor in TV: The Name of the Doctor (which aired weeks after the comic was published), while the Moment would go on to play a role in the 50th anniversary special. On the other hand, the resolution of the Matrix's plotline hinges on the fact that the Time Lords were indeed murdered by the Doctor using the Moment, a sequence of events here relayed not as the personal belief of the Doctor but as objective fact. This notion was famously rejected by The Day of the Doctor, which revealed that Gallifrey had not actually been destroyed but rather exiled to a parallel pocket universe in a way that made it appear to the rest of the universe (Doctor included) as though it was annihilated.
- One of the cover variants depicts Oswin Oswald, who does not appear in the story.
- Clara has a bedroom aboard the TARDIS. The TARDIS later deliberately made it disappear because it was not keen on housing her as a companion. (HOMEVID: Clara and the TARDIS)
- Priyan and Engin talk about Lord President Rassilon's Final Sanction, (TV: The End of Time) on the last day of the Time War. (TV: The Day of the Doctor)
- An incarnation of the Doctor is mentioned to have rejected his name. (TV: The Name of the Doctor, The Night of the Doctor)
- The inside of the TARDIS has been configured into another world before. (PROSE: Cat's Cradle: Time's Crucible)
- The Doctor saves all the old control rooms and their consoles. (TV: The Doctor's Wife)
- The Doctor mentions the Hypothetical Gentleman's attempt to build a quantum resonator. (COMIC: Hypothetical Gentleman)
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