Battle of the Mutara Nebula

The Battle of the Mutara Nebula was the final engagement between James T. Kirk and augment Khan Noonien Singh.
In 2267, Captain Kirk left Khan and his followers on Ceti Alpha V in exile. Because Starfleet or Kirk never returned to check on their progress, there was no knowledge that a catastrophic environmental calamity had occurred, turning Ceti Alpha V into a desert wasteland, mere 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 USS Reliant 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, Captain Terrell and his first officer, Commander Pavel Chekov, were captured by Khan and his followers. He tortured each, and learned not only why they had come to the planet, but also where he may find James T. Kirk. 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

While Admiral Kirk was inspecting the Enterprise, he received a transmission from Doctor Carol Marcus, who was stationed at Regula I. Chekov had hailed her and had told the station that Starfleet was taking control of Project Genesis, under orders from James Kirk. The lie was effective, and Khan knew that Marcus would contact Kirk, asking to confirm the order in person. While en route to Regula I, the Enterprise came across the Reliant, which failed to open communications. Khan opened fire in a surprise attack, severely damaging most of the Enterprise's key systems. 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.

The Enterprise resumed its course to Regula I, and discovered that the science team had been murdered. They also found Chekov and Terrell, as well as the Genesis Device. Khan then intercepted communications, learning the Enterprise would be crippled for days, and decided to maroon Kirk, taking the Genesis Device for himself. This information was falsified, and the Enterprise recovered faster than foretold, with the ship and her crew escaping into the Mutara Nebula, evening the playing ground between the Enterprise and the Reliant.

The Battle

Failing to keep the Enterprise from entering the nebula, Khan allowed himself to be taunted into pursuing Kirk's ship.

Once both ships were inside the Mutara Nebula, they realized 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. Sulu was forced to aim weapons manually, but as he was about to fire, 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, also missing the Enterprise.

Several silent minutes passed, and then both ships saw each other, and both were on a collision course. As the Enterprise performed evasive maneuvers, Khan fired phasers on the Enterprise, disabling one of the ship's torpedo launchers, as well as further damaging the engineering section. This offensive forced Enterprise Chief Engineer Montgomery Scott 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 much of Khan's bridge crew, including his second-in-command in the process.

The Enterprise crew caught Khan by surprise when his ship passed over the Enterprise, which allowed Kirk's ship to ascend behind them, and begin a brief but crippling attack at close range. First, the Enterprise fired a photon torpedo, destroying the Reliant's own torpedo launcher. Second, a phaser burst hit one of the Reliant's warp nacelles, severely damaging it. Finally, a second torpedo was fired, which blew the nacelle off the ship entirely, killing most of the rest of Khan's crew, and maiming Khan in the process. In spite of all this, Khan refused to surrender. 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 its crew could possibly survive the detonation would be to jump to warp, but the ship's main engines were still off-line.

Spock then proceeded to sacrifice 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 surviving Enterprise crewmembers held a funeral for Spock, and sent his body to the newly-formed Genesis Planet in a photon torpedo casing. They then rescued the crew of the Reliant from Ceti Alpha V, and returned to Earth.

The Genesis Planet, off-limits and on the brink of destroying itself, was revealed to be teeming with protomatter, accounting for the planet's instability. This instability manifested itself first in an accelerated rate of growth, then in micro-climatic upheavals. Instead of flourishing, the planet began to experience heavy geologic activity that resulted in the entire surface becoming molten.