Battle of the Mutara Nebula The Battle of the Mutara Nebula was the final engagement between James T . Kirk and Khan Noonien Singh . In 2267 , Captain Kirk left Khan and his followers on Ceti Alpha V in exile . Because Kirk never returned to check on their progress , he had no way of knowing that a catastrophic environmental calamity had occurred that made Ceti Alpha V a desert wasteland , just months after Khan and his followers were left on the planet . Nearly twenty years later , Khan seized an opportunity to achieve what he had wanted for so long : the death of Kirk . Prelude . In 2285 , the was on a survey mission to find a suitable location for Project Genesis , a Federation project to turn an uninhabitable world into an M - class planet . While examining what they thought was Ceti Alpha VI , Capt . Clark Terrell and his first officer , Commander Pavel Chekov , were captured by Khan and his followers . He implanted each with Ceti eel s and learned why they came to the planet . Shortly afterward , Khan and his people took control of the " Reliant " , marooned the crew on Ceti Alpha V , and headed for the Regula I space station . Provocation . Meanwhile , the now - Admiral Kirk was inspecting the when he received a transmission from Dr . Carol Marcus . Chekov already hailed her and told the science team that Starfleet was taking control of the project now , the order coming directly from James Kirk . The ruse was quite effective ; Marcus ' team had been operating independently of the Federation on their project and Khan knew that they would contact Kirk and ask to confirm the order , bringing him to the remote science outpost at Regula I . When communication was broken , Kirk ordered the ship to proceed to Regula I . While en route they came face - to - face with the " Reliant " , which initially failed to open communications . In a serious lapse in judgment , Kirk disregarded Starfleet regulations dictating a defensive posture when encountering a non - communicative ship . As a result , Khan opened fire in a surprise attack , severely damaging most of the " Enterprise " s key systems , notably weapons , shields , and propulsion . Khan then hailed Kirk , agreeing not to destroy the " Enterprise " on condition that Kirk would hand over both himself and all of the information on the " Enterprise " computers relating to Project Genesis . Kirk pretended to comply , but instead he and Spock entered the " Reliant " s prefix code , lowered its shields and returned fire . With " Reliant " s photon torpedo launcher and warp drive disabled , Khan was forced to withdraw . Some time after the battle , the " Enterprise " engineering team was able to restore auxiliary power and the ship resumed its course to Regula . When Kirk and an away team boarded Regula I , they found that the science team had been murder ed . They also found a traumatized Chekov and Terrell in a closet . The away team and the two " Reliant " officers then beamed down to the planetoid and discovered the Genesis device , along with Carol and her son David Marcus . Khan , still controlling Chekov and Terrell through the Ceti eels , ordered them to kill Kirk . However , Terrell turned his phaser on himself and Chekov ' s eel exited his body . Upon learning from intercepted communications that the " Enterprise " would be crippled for days , Khan decided to maroon Kirk on the planetoid while taking the Genesis device for himself . However in doing so , Khan made a major mistake . For the predictions Spock gave about repairs were in a deceptively simple code that simply stated that the time needed for repairs was actually in hours and the crew managed to repair the weapons and impulse engines although only partial main power was available . They beamed the landing party back and Kirk ordered the ship go to battle stations . With the damaged " Enterprise " still outmatched by the " Reliant " , both in terms of firepower and speed , Spock advised that they proceed to the nearby Mutara Nebula , where the odds between both ships would become even as the static discharge from within the nebula would severely impair the effectiveness of the sensors and render a ship ' s shields completely inoperable . The Battle . The " Enterprise " fled towards the nebula , with the " Reliant " in pursuit , even firing a photon torpedo that deliberately missed the " Enterprise " s starboard nacelle pylon as a deterrent against going into the nebula . However , knowing the limitations of fighting within the nebula , the " Reliant " refrained from entering until Kirk opened communications and taunted Khan into pursuing the " Enterprise " into the nebula . Once they entered , both ships found that their shields were disabled and their visual and tactical systems were severely impaired . The conflict became a game of " hide and seek " , with both vessels firing at each opportunity they got . On the second opportunity of firing , the " Enterprise " was just aft of the " Reliant " but because phaser locks were rendered inoperable by the nebula , Sulu had little alternative but to aim them manually . As he was about to fire upon the " Reliant " , the " Enterprise " was rocked by storm activity within the nebula , jogging Sulu ' s aim and the phaser fire narrowly missed the " Reliant " . In retaliation , the " Reliant " fired a torpedo from one of its aft launchers , comfortably missing the " Enterprise " . Some minutes passed with no conflict until both ships saw each other almost on a collision course and as the " Enterprise " performed evasive maneuvers to starboard , Khan fired phasers on the " Enterprise " , disabling the " Enterprise " s port torpedo launcher and further damaging the engineering section , forcing Scotty to take main power off - line due to radiation leakage . The " Enterprise " was able to inflict significant damage to " Reliant " as well in the short firefight , firing phasers hitting just behind the bridge , killing Khan ' s first man , Joachim in the process . Spock told Kirk that although Khan was intelligent , his critical weakness was his inexperience - his attack pattern indicated just " two - dimensional thinking " , not considering attacking from above or below , only on the same plane . Having realized this weakness , Kirk ordered the ship to descend vertically and stand by on photon torpedoes . After returning to the bridge from medical treatment , Chekov offered his assistance to Admiral Kirk . Kirk ordered Chekov to the weapons console . The " Enterprise " crew caught Khan by surprise when his ship passed over the " Enterprise " , which allowed Kirk ' s ship to ascend behind the enemy and begin its brief but crippling onslaught on the " Reliant " at close range - first a photon torpedo was fired from the starboard launcher , destroying the " Reliant " s own torpedo launcher . Secondly , a phaser burst hit the " Reliant " s port warp nacelle , severely damaging it and finally a second torpedo was fired , blowing the nacelle off the ship and killing most of Khan ' s crew and maiming Khan in the process . In spite of the severe damage that the " Reliant " had sustained and severe physical injuries , Khan was not ready to surrender yet . Commander Uhura hailed the " Reliant " , demanding its immediate surrender , but as a final act of vengeance a dying Khan activated the Genesis Device , which would reorganize all matter in the nebula , including the " Enterprise " . The only way the " Enterprise " and the crew could possibly survive the detonation ( 4 minutes from Khan ' s activation ) would be to jump to warp , but the ship ' s main engines were still off - line . Thinking about a philosophical conversation that he had with Kirk previously , Spock sacrificed himself to save the ship and its crew . In the radiation - contaminated engine compartment , Spock managed to reconnect power to the warp engines . The " Enterprise " jumped to warp seconds before the " Reliant " exploded . The detonation of the Genesis Device re - organized the matter within the Mutara Nebula and created a new planet designed by the Device ' s matrix . Aftermath . The " Enterprise " held a funeral for Spock and sent his body to the Genesis Planet in a photon torpedo casing . They rescued the crew of the " Reliant " from Ceti Alpha V and returned to Earth . Just before he died , Spock transferred his " katra " to Dr . Leonard McCoy . In order to return Spock ' s " katra " to , they would need to recover his body and return it to Mount Seleya , but the Genesis Planet had since been declared off - limits due to the controversy surrounding the use of the Genesis Device - the Klingon Empire feared that the Federation could use it as a weapon . However , Kirk , willing to sacrifice his career to save Spock , gathered his command crew and returned to the Genesis Planet . Saavik and David were there on a mission to survey the planet , but their ship was destroyed by Klingon s , eager to get information on the device . Meanwhile , Spock had been reborn by the Genesis effect , but was suffering rapid aging . The planet was on the brink of destroying itself when Kirk arrived but the " Enterprise " was disabled by the Klingons . Faced with a boarding party , Kirk activated the auto - destruct sequence . Beaming to the planet , Kirk was able to retrieve Spock , but his son David was killed and the " Enterprise " was destroyed . Kirk managed to beam himself and the others to the Klingon Bird - of - Prey and escaped just as the planet was destroyed . With a ceremony on Vulcan , they were able to reunite the body of Spock with his " katra " . Appendices . Background information . The battle as ultimately visualized , was conceived by Production Designer Joe Jennings and Art Director Mike Minor . At the " Star Trek Designers Talk Trek History At Art Directors Guild Event " in 2009 , Jennings recalled how the battle was originally scripted as having the two vessels pounding at each other at close range in open space . He considered the battle thus scripted – likening it to a man - o ' - war slugging match from the era of sail – ludicrous , pointing out that , more realistically , spaceships would go at each other in high - speed passes under open space circumstances ( as was adopted in the Battle of Wolf 359 and Dominion War battle scenes in their respective , later episodes , as well as in the films , most notably ) . Together with Minor he came up with the concept of the Mutara Nebula knocking out both ship ' s navigational and tactical systems as a more believable rationale for the slower paced close quarter combat between the two vessels , which was ultimately accepted by the writing staff . After the sequence was filmed , Jennings gleefully recalled Director Nicholas Meyer ' s reaction , " " You were right . Thanks for not saying so ! " " ( " " ) An element in the battle he considered equally ridiculous , but was not able to change , were the handlings performed in the torpedo bay – as the photon torpedo s should have been fired directly from storage . In an interview in the " " - special feature , " Designing Khan " , he said that seeing the ensign s with hooks pulling the grating off the torpedo conveyor before launching it drove him crazy , since any real ship that took that long to load weapons would probably be destroyed in about ten seconds . Coincidentally , his concerns in this respect were later addressed by Meyer in , where it was indeed strongly implied that torpedos were fired directly from storage in in which Captain Montgomery Scott uttered the line , " " Negative , Captain . According to Inventory we ' re still fully loaded . " " , after the " Kronos One " was unexpectedly hit by a torpedo volley from the " Enterprise " s torpedo bay . Ironically , the battle was three decades later exactly re - enacted as originally scripted , including the sailing ships imagery ( albeit flying ones ) that it had conjured up with Jennings , in the 2011 version of " The Three Musketeers " , where the " Star Trek " battle was paraphrased as a pop culture reference . Apocrypha . According to the computer game , " " , a recreation of this battle is now a standard training simulation at Starfleet Academy . Its primary educational purposes are to reinforce the importance of taking proper precautions when approaching a non - communicative ship ( even a Starfleet vessel ) and then to practice space combat in poor sensory conditions .