Assimilation² ( comic story ) Assimilation ( full indicia title Star Trek : The Next Generation / Doctor Who : Assimilation ) is an eight - part crossover comic book mini - series between the " Doctor Who " and " Star Trek " franchises , primarily featuring characters from " " but also the original " Star Trek " . It began publication on 30 May 2012 in North America . As of 2018 , it is the only officially licensed crossover between the two franchises , though it remains non - canon in the " Star Trek " franchise . 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 , 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 ! Plot . 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 before attacked without calling for their target ' s surrender , nor have they attacked so brutally . A Starfleet officer notes that the Borg are not working alone — they are joined by a cybernetic race the Federation have not encountered before . At that moment , the Borg and their new allies beam into the command centre to attack and assimilate Deltans and Starfleet officers . The Prime Minister and three Starfleet officers escape to the USS " Mattingly " , a Starfleet Runabout , and leave the planet alongside other Starfleet ships . In ancient Egypt on Earth , the Eleventh Doctor , Amy and Rory are engaged in a chariot chase with the Pharaoh ' s palace guards , who pursue 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 , then attacks the Pharaoh . He then changes into his true form , revealing himself as a shape - shifting 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 destroy 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 — Cybermen and Borg . The TARDIS rumbles , Amy and Rory stumble , but the Doctor maintains control , saying that they ' re " almost there . " They step out of the TARDIS in San Francisco , about 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 . Issue 2 . While completing a routine scan of Data ' s neural net , Geordi La Forge and Data discuss the philosophical implications of their technological upgrades . Captain Picard sends Commander Riker on a mission to check on mining operations on Naia VII , an aquatic world . Riker takes Data and Worf with him . On the planet , they meet Captain Ochoa and Lt . Amato , two members of the Starfleet Corps of Engineers who are leading the mining operation , and Seelos , one of the indigenous , amphibious Dai - ai . Since the planet is largely covered in water , the mines are drilled from the tops of mountainous islands . Captain Ochoa , in charge of the mining operations , explains the difficulties of mining below sea level , and notes his concerns that " safety isn ' t the no . 1 priority " . A pressure compartment suddenly fails and the section that Riker and his team are in floods . Worf rescues Ochoa and Amato , and Data rescues Riker . In the aftermath of the flooding , Dr Crusher tells Capt . Picard that eight people died and twenty - two were injured . Geordi tells Picard that the mine has been operating with very low safety protocols , but were under heavy pressure from Starfleet to meet regular quotas . Picard tells him that the pressure is due to the need to rebuild the fleet after the loss to the Borg at Wolf 359 . After Riker returns to the ship , Picard tells him that upgrades to the ship ' s holodeck have been completed , and a new Dixon Hill adventure awaits him . Riker , Data and Crusher don 1940s attire and begin the programme . They hear the Doctor ' s TARDIS materialise , but put it down to a bug in the upgrade . The Doctor , Amy and Rory meet the Starfleet officers in a bar , where the Doctor immediately recognises Data as an android . Riker and Crusher assume that the Doctor , Amy and Rory are holodeck characters and the holodeck is malfunctioning again . Riker ends the programme and is surprised to see the TARDIS and its three occupants still present . Worf escorts the trio to the ship ' s observation lounge . The Doctor recognises him as a Klingon , but notes that his memories are being altered . Before he saw Worf , the Doctor had never heard of them . In the observation lounge , Picard introduces himself to the Doctor , who notes that they " shouldn ' t be here , really . " Deanna Troi scans the TARDIS travellers ' minds , saying that Amy and Rory are slightly nervous but completely trusting of the Doctor , and sensing wisdom and sadness in the Doctor , but no ill intent . Picard is slightly sceptical . The conversation is interrupted by news of the attack on Delta IV . When the attacking fleet is put on screen , Picard recognises the Borg and the Doctor recognises the Cybermen . The Doctor says , " We shouldn ' t be here , Captain . " Picard replies , " I believe you ' re right . . . " Issue 3 . A Cybercontroller fitted with Borg technology hails the " Enterprise " and says , " You have no means of stopping us . " Knowing that they will not be able to fight off the entire Borg / Cyberman fleet , Captain Picard orders the " Enterprise " to retreat and hide in the nearby Paertes Nebula . The Doctor tells Picard and his crew about the Cybermen , and Data scans the ship ' s historical database for any record of them . He finds a log entry from the " Constitution " - class " Enterprise " , commanded by James T . Kirk . As Data begins to relay the contents of the log , the Doctor is overcome with a flood of new memories . . . Stardate 3368 . 5 : Captain Kirk , Spock , McCoy and Scotty investigate a Federation archaeological team on Aprilia III that has lost contact with Starfleet . Upon landing in a shuttlecraft , they are greeted by project manager Jefferson Whitmore , who assures them that all is well and gives them a tour of the facility . Kirk finds the staff suspiciously calm . His team returns to the facility after dark . Trying to bypass an electronic lock , they are greeted by a strange man in a long scarf . He introduces himself as " the Doctor " , opens the lock with his sonic screwdriver and offers jelly babies to the Starfleet officers . They find the researchers standing catatonically , with small cybernetic devices in their ears . Dr McCoy begins to remove the devices and revive the crew , but is interrupted by the arrival of a Cyber - Leader and two Cybermen . A firefight ensues , but the Starfleet phaser s are ineffective against the Cybermen . The Doctor uses the gold cover from Kirk ' s communicator to clog the Cybermen ' s respiration . After the Cybermen are defeated , the Doctor slips quietly away . The alien equipment that the archaeologists were investigating appears dormant , but it is not . On Picard ' s " Enterprise " , the Eleventh Doctor remembers his meeting with Kirk , but also remembers " not " remembering it . The Cybermen appear to have abandoned their pursuit of the " Enterprise " . Captain Picard takes the Doctor , Amy and Rory to meet Guinan . Issue 4 . In Ten Forward - the " Enterprise " ' s lounge and recreation facility - the Doctor is introduced to Guinan , the bartender , and they speak about the Borg - Cybermen alliance . Oddly , Guinan and the Doctor seem to be familiar with each other , which can be attributed to the fact that both are time - and space - sensitive ( as the Doctor is a Time Lord and Guinan is El - Aurian . ) Guinan also knows the Cybermen and the Doctor come from another universe , and it seems the Cybermen brought the two universes together and will cause Armageddon on a galactic scale . Captain Picard receives a message from Commander Riker and the Doctor makes haste to the briefing room as well . The captain still does not trust the Doctor , but Guinan assures him the Doctor can be trusted - to which Picard says he reminds him of her since he does not know the true identity of either . However , it now seems that at first the alliance was heading to Earth but changed course . Data tells them the Borg - Cybermen went to the planet Cogen V . Picard decrees they go there at once and send down an Away Team . The Doctor asks that he , Amy and Rory join the Away Team as he is the only one with knowledge of the Cybermen , to which Picard agrees reluctantly . The three of them join Riker , Worf and Data on a transporter pad and are all fascinated by it as the transporter energizes . The Away Team comes under fire soon after successfully beaming down to Cogen V , but the group neutralises the attackers with a combination of phasers and the sonic screwdriver . They find that their attackers were sentry drones that serve to defend the planet - and that there are Borg and Cybermen corpses around them . Commander Riker orders that a body of each species be taken back to the Enterprise to learned what happened on the planet , and The Doctor even brings one of the sentry drones to learn more . In the sick bay , Dr Crusher performs an autopsy on both bodies and is shocked to learn that the Cybermen still have human brains . Off to the side , Counsellor Troi meets the Ponds and simply introduces herself by her first name - Deanna . She asks if the Doctor takes them on adventures , and they confirm it and tell her of their journeys with the Doctor . Troi also brings up another thing she sensed - that they are as protective of him as he is of them , to which Amy admits the Doctor is alone in the universe and he needs them more than they need the Doctor . Meanwhile , the Doctor , Data , Dr Crusher and Geordi LaForge have been at work on the Borg and Cybermen bodies that were recovered . LaForge uses his VISOR in an effort to gain further insight and discovers something after examining both bodies : the Borg and Cybermen were killing each other . It seems an unbelievable prospect - but the Doctor is able to recover and display a video clip from the sentry drone that confirms this . Lt . Worf calls for the captain to the bridge and tells him the Borg have contacted them . The Borg wish to speak to Locutus about the possibility of a truce . The captain cuts the transmission saying there will be no truce . The Doctor tries to convince him but Picard is adamant that there will be no truce . Issue 5 . The Doctor pleads with Captain Picard to open negotiations with the Borg , but the captain grimly refuses . The Doctor cannot understand his reasons , so then Guinan comes to Picard ' s ready room to tell the Doctor of his grim fate with the Borg some years ago . There , they learn that not only was Picard temporarily assimilated and named Locutus , but because of his knowledge of Starfleet tactics , thirty - nine starships and over eleven thousand Starfleet officers were lost at the battle of Wolf 359 . These memories and experiences that Captain Picard was forced to endure still haunt him . The Doctor finally understands now , but he still cannot break through to Picard , who wishes to return to Earth to aid in the rescue operations for the planets that already fell to the Borg and Cybermen . In the sickbay Rory has to marvel at the advanced medical facilities that Doctor Crusher has . However the Doctor arrives there to tell the Ponds that Picard will not listen to reason . He fears that he and his companions will have to ally with the Borg or fight the Cybermen themselves . However Counsellor Troi tells the Doctor that maybe another person can make Picard listen to reason . Amy goes to Picard ' s ready room to tell him that she along with the Doctor and Rory are going to confront the Cybermen themselves . Picard protests such an action , but Amy then tells Jean - Luc of the day she first met the Doctor . He met her when she was but a child and later in her life when she aged to her twenty ' s , and can see that he hadn ' t aged a day . She then brings Picard to the holodeck where the Doctor brings Picard into his TARDIS . Picard marvels at this almost unbelievable technology . The Doctor takes Picard to the future and begins showing Picard the horrible events to come if they don ' t stop the Cybermen . At first Picard believes this all to be an illusion created by the Doctor , but he assures Picard it is not . Soon Qo ' Nos , the capital of the Klingon Empire , is assimilated by the Cybermen . They soon go slightly further into the future and see that Vulcan , the Judoon , and even the world of Raxacoricofallapatorius and its people are assimilated . Then going even further into the future both see that Starfleet Academy was the last vestige of free people left in the universe . It soon fell though and the last remnants of humanity march in to be upgraded by the Cybermen . With what Picard saw and some wise words from the Doctor , Jean - Luc finally concedes and will go against his judgment and ally with the Borg . Issue 6 . The Doctor , Amy , Rory , Picard , Riker , Worf and Data beam down to the desolate planetoid Tau Lee where they meet a party of Borg led by a drone who calls himself the Conduit and agree to be allies against the Cybermen . At first there is a bit of hostility as the Conduit was once a friend to Commander Riker . His ship was destroyed , which led to his assimilation by the Borg . The Doctor outlines a plan to catch up with the Cyberfleet heading towards the Borg homeworld and restore the Borg ' s executive library that was destroyed by the Cybermen which has rendered most of the collective inert . To get a copy of the library , he proposes travelling back in time . With Picard and the ship ' s counsellor , the Doctor goes to Naia VII to try to get supplies of gold , an effective weapon against the Cybermen , but the humans are unable to help as their agreement with the Dai - ai prevents them from mining for it . Picard begins talks with Seelos , leader of the Dai - ai , but it is the Doctor who swings the deal before travelling back in time with Amy and Rory to the Battle of Wolf 359 . There , aboard a Borg cube , they encounter Captain Picard assimilated into the Borg collective as Locutus . Issue 7 . Locutus ignores the time travellers and they proceed through the Borg ship to a computer terminal where the Doctor copies the executive libraries . As the battle begins , the travellers slip back to the TARDIS and return to the Enterprise . Geordi the engineer has bad news , though , as , despite Borg enhancements suggested by Conduit , the Enterprise cannot achieve sufficient speed to catch the Cyberman fleet before it reaches the Borg homeworld . However , the Doctor suggests boarding the Cybership in the TARDIS . Once aboard , though , they are detected almost immediately despite splitting into two parties and soon find themselves up against the collected might of the Cybermen . Issue 8 . Worf ' s party , which includes Amy and Rory , attacks the engine room and manages to disable the engines . The Doctor ' s party , meanwhile , which includes the Conduit , Picard and Data , is captured by the Cybermen , but they are rescued by the arrival of the Enterprise firing a gold - infused particle beam . This destroys the Cybermen but not the Cyber Controller who is instead restrained by Data and the Conduit . This allows the Doctor to restore the Borg executive libraries . Immediately , the Borg set all Cyberships to self - destruct . They all race back to the TARDIS before the fleet explodes , but then Conduit announces an end to the alliance and attempts to assimilate the TARDIS . However , the TARDIS retreats from the attack , entering Data . Data fights back then Rory and Worf physically throw Conduit into the time vortex , ending the threat . With the Cybermen destroyed , the universes revert to the way they should be and the Doctor , Amy and Rory depart for their own universe . However the Doctor begins to suspect something is wrong before he leaves back to his universe . As the Borg have been brought back online , they believe in order to assimilate the Doctor they must master time travel .