Tesseract was the third part of the story arc begun in Doctor Who (2009) #1. It was divided into two chapters: "Time Smash" and "Implosion".
While the Tenth Doctor gives his new companions, Emily Winter and Matthew Finnegan, a tour of the TARDIS, the vessel is invaded by a number of dimension-hopping aliens. The Advocate places doubt into Matthew Finnegan's mind about the Doctor's morality, while the Tef'Aree have much the same effect upon Emily Winter. Meanwhile, the proximate cause of the invasion — the breech of the TARDIS by the Acari spaceship —forces the TARDIS interior to rearrange itself. Because the Doctor is psychically linked to the TARDIS, this trauma causes the Doctor to undergo temporary mental instability and his past selves begin to bleed through. Only by disengaging from the Acari ship and quickly restoring the proper console room will the Doctor's tenth persona fully reassert itself.
When Emily finds the right console, order is restored. But the Doctor's superphone rings before they can enjoy their victory. Martha Jones calls with an urgent appeal for the Doctor to return to Earth and help UNIT solve a mysterious new problem . . .
- The Shadow Proclamation is mentioned.
- The Doctor is shown simultaneously wearing elements of the Sixth and Fifth Doctor's outfits, as well as the Fourth Doctor's scarf, the Seventh Doctor's hat and the Eighth Doctor's cravat.
- Donna Noble is mentioned.
- The Cloister Bell sounds.
- The Doctor offers his companions a Mickey Mouse watch.
- Vislor Turlough kept a diary in the TARDIS, which Matthew discovers.
- When the Doctor answers his superphone he initially wonders if Lady Christina might be phoning him.
- The Tef'Aree predict a number of events in Emily's future, including her standing beside a memorial to a dead friend and an encounter with "the Soul Free".
- The Doctor got Martha and her husband a wedding gift which reacted badly with champagne and sent her mother to the ceiling. She is filling in as UNIT's scientific advisor while Malcolm is in Geneva.
- The story takes place almost entirely within the TARDIS. Only a handful of stories have explored the interior of the TARDIS, including the television stories The Invasion of Time, Castrovalva, The Doctor's Wife, and Journey to the Centre of the TARDIS as well as the comic story Changes.
- This story was reprinted in the IDW graphic novel Tesseract.
- The Advocate implies the TV stories Earthshock and Terminus are only a week apart.
- The Doctor visits many of the TARDIS's old console rooms, (TV: The Masque of Mandragora, Doctor Who, An Unearthly Child) as well as the art gallery and swimming pool; (TV: The Invasion of Time) he assumes there were two pools, since he deleted the other one. (TV: Paradise Towers)
- The Doctor's wind-up mouse is used and is mistaken for K9 by the Acari. (TV: The Doctor's Daughter)
- At one point, the Doctor spews quotes from various previous adventures. (TV: State of Decay, The Ultimate Foe, An Unearthly Child)
- The tribophysical waveform macrokinetic extrapolator is used to disengage the TARDIS from the Acari ship. (TV: Boom Town)
- The Doctor refuses to allow Emily to take possession of Jack Harkness' sonic blaster as he says it is reserved for "someone else". (TV: Silence in the Library/Forest of the Dead)
- Adric is mentioned several times, including a reference to his death, which is recalled in detail. (TV: Earthshock)
- Malcolm Taylor and Captain Magambo are namechecked by Martha Jones. (TV: Planet of the Dead)
- Emily arms herself with the Fifth Doctor's cricket bat. (TV: Castrovalva)
- The notion of the TARDIS existing in a state of temporal grace is mentioned. (TV: The Hand of Fear)
- The TARDIS architecture has previously been tampered with by outside forces. (COMIC: The Mark o Mandragora)