USS Reliant fires phasers, scoring a direct hit on the Enterprise's port torpedo launcher
Captain Kirk loses his best friend
After a brief engagement near Regula I, the Enterprise escaped into the surrounding Mutara Nebula, with the Reliant in pursuit. The Reliant refrained from entering, knowing the limitations of fighting within the nebula. However, Kirk opened communications and taunted Khan to make him pursue 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 "cat and mouse", with both vessels firing at each opportunity they got. Khan opened fire first with a photon torpedo narrowly missing the Enterprise's starboard nacelle pylon. 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 a storm 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 damage on the 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 weakness was his inexperience - his attack pattern suggested that he was only thinking "two-dimensionally", not considering attacking from above or below, only on the same plane. 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 destroying the nacelle, killing most of Khan's crew and maiming Khan in the process. In spite of the severe damage that the Reliant had sustained, Khan was not ready to give up yet.
Cmdr Uhura hailed the Reliant demanding their immediate surrender but as a final act in the hope of getting his 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 decided to sacrifice himself to save the ship and its crew. In the contaminated engine compartments, 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.