Assimilation² (comic story)

Assimilation2 was a Doctor Who/Star Trek: The Next Generation comic mini-series that began publication on 30 May 2012 in North America. It was the first officially licensed crossover between the two franchises.

Publisher's summary
The two greatest science-fiction properties of all time cross over for the first time in history! When the Federation's most terrifying enemy strikes an unholy alliance with one of the Doctor's most hated antagonists, the result is devastation on a cosmic scale! Spanning the ends of space and time itself, Captain Jean-Luc Picard and the crew of the USS Enterprise find themselves joining forces with the time-travelling Doctor and his companions, with the fate of the galaxy hanging in the balance!

Issue 1
Stardate 45635.2: The planet Delta IV is invaded suddenly and without warning by the Borg. The Prime Minister of Delta IV and her Aide are beamed to a secure command center where they observe the invasion alongside Starfleet personnel. The Prime Minister notes the atypical nature of this invasion - the Borg have never attacked without calling for their target's surrender before, nor have they attacked so brutally.

A Starfleet officer notes that the Borg are not working alone — they are joined by another cybernetic race the Federation have not encountered before.

At that moment, the Borg and their new allies beam into the command center and begin attacking and assimilating Deltans and Starfleet officers. The Prime Minister and three Starfleet officers escape to the U.S.S. Mattingly, a Starfleet Runabout, and leave the planet alongside other Starfleet ships.

Meanwhile, on Earth in ancient Egypt, the Doctor, Amy and Rory are engaged in a chariot chase with the Pharaoh's palace guards, who are pursuing them with vigor.

Passing a market stall, the Doctor grabs one of the support beams and pulls it out of the ground. Fruit and baskets fall in front of the palace guards, stopping them dead. The trio continue their journey to the Pharaoh's palace.

Once in the palace, the Doctor, Amy and Rory attempt to stealthily make their way to the Pharaoh's throne room. Rory accidentally knocks over and breaks a large blue vase, attracting more of the palace guards. As the guards move in, the Doctor climbs up to a curtain rail and uses the sonic screwdriver to detach it from the wall, pulling it down and over the guards.

The three move quickly to the entryway to the throne room, where Rory talks his way past the guards and into the throne room.

The Pharaoh asks how the three could have gotten into the throne room. The Pharaoh's Vizier claims they have "clearly gone mad from the desert heat" and says he will dispatch them. He demands to know the Doctor's name. The Doctor says the Vizier will know him better by his race — Time Lord. The Vizier is shocked, reacts disbelievingly and attacks the Pharaoh. He begins to change into his true form, revealing himself to be a shape changing alien.

The Doctor retrieves a small green crystal, an "interdimensional prison cell", and uses it to "trap" the Vizier. He informs the Pharaoh that the Vizier was in fact an escaped alien criminal who was planning to "harness the kinetic energy from the Nile to fire up a tachyon pulse inverter" and destroyed half of the Earth in the process.

Back in the TARDIS, the Doctor states he'd like to go somewhere "cool. And foggy." Rory hands the Doctor the green crystal and there is a flash of imagery - the Borg. The TARDIS rumbles as Amy and Rory stumble, but the Doctor maintains control, saying that they're "almost there."

They step out of the TARDIS in San Francisco, circa 1945. Rory and Amy are wearing period-appropriate clothing and the Doctor states this was his intended target all along. He describes San Francisco as a "bubbling cauldron of capers and investigations" and advises his companions that they're "bound to run into something unusual here."

At this point they step into a bar where they see an Android in a pinstripe suit.

Characters from the Doctor Who universe

 * Eleventh Doctor
 * Amy Pond
 * Rory Williams
 * Unnamed Egyptian Pharaoh
 * Unnamed alien criminal
 * Cybermen

Characters from the Star Trek universe

 * Lieutenant Commander Data
 * Commander William Riker
 * Doctor Beverly Crusher
 * Prime Minister of Delta IV
 * Unnamed Aide to the Prime Minister of Delta IV
 * Jahson
 * Unnamed Starfleet Admiral
 * The Borg

Companions

 * Rory Williams' time spent as an Auton Roman soldier has left him experienced with steering chariots and, apparently, intimidating Egyptian soldiers.

The Doctor's TARDIS

 * The TARDIS experiences some "dimensional feedback" when it arrives on the Holodeck of the Enterprise-D.

Technology

 * Prisoners of some facilities used by the Atraxi, the Shadow Proclamation and the Visendi Detention Complex are transported in small green crystals, referred to by the Doctor as an "interdimensional prison cell and interstellar delivery service, all at once." The size of the crystals suggests some manner of compression technology not dissimilar to those of the Teselecta or a Slitheen skinsuit. The crystal containing the unnamed alien prisoner apparently fell to Earth, suggesting it was either being transported or that the crystals have the ability to propel themselves through space.
 * Issue 1 ends with the TARDIS materializing inside the USS Enterprise's Holodeck, a room on board the vessel that combines computer graphics and replicator technology to simulate realistic environments. In the Star Trek franchise, Holodecks are primarily used for recreational pursuits and training.
 * The Doctor recognises Lieutenant Commander Data as an android.

Continuity

 * The Doctor wonders aloud if the escaped alien prisoner was heading to an Atraxi prison or a Shadow Proclamation facility. He concludes the alien is most likely heading to "the Visendi Detention Complex."
 * The alien prisoner is able to change its form as could Prisoner Zero, (DW: The Eleventh Hour) though its "normal" form is markedly different.

The Doctor, Amy and Rory

 * Rory's memories of being an Auton soldier and references to the companions being married place this post-DW: The Big Bang

Enterprise crew

 * Stardate 45635.2 places "Assimilation²" between the  episodes "" and "".