The Battle of Mutara was the final engagement between James T. Kirk and the centuries old Sith Lord Khan Noonien Singh. In 22 BBY, 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 fifteen years later, Khan seized an opportunity to achieve what he had wanted for so long: the death of Kirk.
In 19 BBY, the Republic starship Reliant was on a survey mission to find a suitable location for Project Genesis, a Federation project to turn an uninhabitable world into a habitable one. 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 eels 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.
Meanwhile, the now-Admiral Kirk was inspecting the Enterprisewhen 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 Republic military 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 murdered. 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 away team 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 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. Khan opened fire first with a photon torpedo narrowly missing. 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 relentless 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 blast hit the Reliant's port warp nacelle, severely damaging it and finally a second torpedo was fired, completely severing the nacelle from 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.
Reliant, one of her engines destroyed, and heavily damaged, adrift in the nebula Commander Uhura hailed the Reliant, demanding its immediate surrender, but as a final act of vengeance a dying Khan activated the Genesis Device. For the Enterprise and its crew to survive the detonation of the Genesis Device (in four minutes from Khan's activation), the ship's warp drive would have to be engaged but it was still off-line. Thinking about a deep 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, however, was resucitated by Dr. McCoy before he died. 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.