The Battle of Altamid was an engagement between the Federation starship USS Enterprise and a massive fleet of single-crew vehicles commanded by Krall, which culminated in the destruction of the Enterprise and the capture of her crew.
On stardate 2263.02, a disassembled ancient bio-weapon called the Abronath was to be presented to the Teenaxi as a token of goodwill from Captain James T. Kirk, acting as a neutral intermediary of the Fibona. The Teenaxi refused to accept the artifact and the Abronath was stored in the vault of the Enterprise. Krall sought to use the weapon to attack the Federation. He hijacked the Federation's Magellan probe and gained access to Starbase Yorktown's communications systems and the logs of all nearby vessels, including the Enterprise and knew they carried the Abronath aboard. An agent of Krall's, Kalara, was dispatched to Starbase Yorktown to lure the Enterprise to Altamid under the pretense of rescuing her trapped crew in order to secure the Abronath for himself.
Because Altamid laid beyond the Necro Cloud nebula, the Enterprise was cut off from communication with Starfleet. Upon arrival at Altamid, Ensign Pavel Chekov detected a proximity alert - an unknown "ship" which refused to answer the Enterprise's hails. This "ship" turned out to be a large swarm of tiny ships, working as one until they were ready to attack. Captain Kirk immediately realized the threat posed by the swarm and ordered the Enterprise to red alert and its shields raised. The swarm moved in on the Enterprise, which began firing its phasers and photon torpedoes at will; however, the phasers proved only minimally effective due to the sheer number of the swarm ships, and the torpedoes were unable to hit them due to their small size. Commander Spock quickly advised Captain Kirk that the Enterprise was not equipped to adequately combat the swarm just as hundreds of Krall's ships slammed into the Enterprise's navigational deflector dish, their numbers instantly overwhelming the starship's shields and completely destroying it. Captain Kirk ordered the ship to warp away from the vicinity in desperation even without this critical system operational. However, this order proved futile as the swarm proceeded to attack the nacelle pylons, completely severing the nacelles from the stardrive section and destroying the Enterprise's warp capability.
With only sub-light travel possible, Chief Engineer Montgomery Scott attempted to reroute power from the warp core to the impulse engines in order to getting the engines functional again. The swarm ships lodged in the Enterprise hull began sending boarding parties aboard, led by Manas, killing numerous crewmembers. Kirk ordered the crew to take defensive action against the intruders, with Mr. Spock and Dr. Leonard McCoy leaving the bridge to assist. Krall himself soon boarded the ship in search of the Abronath. Spock realized Krall's intent and alerted Kirk who left command of the bridge to Lieutenant Hikaru Sulu to secure the artifact while McCoy found several crewmembers, either dead or close to death, "drained" of their life signs in attacks from Krall.
With power from the warp core diverted to the impulse engines, the Enterprise attempted to head back towards the Necro Cloud in an attempt to lose the swarm. In response, Krall ordered the swarm to cut the Enterprise's "throat," the slender pylon connecting the primary and secondary hulls. As they had done to the nacelles, the swarm collided with the neck section of the Enterprise, detaching it from the stardrive section, cutting off the impulse engines from the warp core. Complicating matters, a portion of the neck section was still connected to the saucer causing the damaged impulse control computer to continue to attempt to draw power from the disconnected warp core. Mr. Spock and Dr. McCoy were ejected clear of the Enterprise in a turbolift, whose shaft connected to the stardrive section. With it separated from the rest of the ship, the turbolift car dropped into open space. It was subsequently impacted by a swarm ship, but Spock and McCoy were able to commandeer the craft.
The surviving crew in the heavily damaged saucer section realized that only by manually executing saucer separation protocols and freeing the primary hull from the neck section would the impulse engines be forced to accept power from the saucer's fusion generators. Kirk set out to separate the ship but was intercepted by Krall, who battled the captain hand to hand for control of the Abronath. On the bridge, Lieutenant Nyota Uhura, realizing that Kirk must have encountered resistance en route ventured to the neck section to help Kirk engage the separation sequence. Although Uhura was able to engage the saucer separation, she was ultimately trapped in the separated neck section with Krall, who took her captive. Despite the separation, the damage to the Enterprise's saucer was still severe. With structural integrity and inertial dampers failing, Kirk ordered the surviving crew in both separated sections of the vessel to abandon ship. He also took the opportunity to hide the Abronath in the cranial cavity of Ensign Syl to prevent it from falling into Krall's hands. In the commandeered swarm ship, Dr. McCoy realized that Krall's forces had begun capturing the escape pods and headed towards Altamid to avoid imprisonment. Scotty, in a last ditch effort to avoid the boarding parties, equipped himself with a respirator and encased himself in an advanced long-range photon torpedo which was fired from the torpedo launcher and headed towards the surface of the planet. Kirk returned to the bridge and realized the saucer was doomed. He ordered Sulu, Chekov and Kalara to evacuate in Kelvin pods with him close behind. Sulu was subsequently captured by a swarm ship while Kirk, Chekov and Kalara landed safely on Altamid as the Enterprise herself entered the atmosphere and crash landed.
With Krall's forces having captured most of the Enterprise crew, Kirk, Chekov and Kalara were able to locate the ruined saucer module with the intent of returning to the main bridge and repairing the ship's sensors to locate the crew. With the science station still intact, Chekov was able to reroute enough power to locate the crew. Kirk led Kalara to where he claimed he had hidden the Abronath, but Kalara betrayed the captain and alerted Krall. However, Kirk had predicted Kalara's duplicity and led her and several of Krall's drone warriors in a firefight through the corridors of the destroyed ship. Trapped, Kirk used his phaser to ignite the saucer's thruster fuel, the resulting detonation causing the saucer to begin to rise and throw Kalara and the drones off balance, allowing Kirk and Chekov a chance to escape. Blasting through the viewscreen on the bridge, Kirk and Chekov slid towards the surface on the rising saucer with Kalara in pursuit. Unfortunately for her, the saucer section continued to rise, ultimately crushing her as it completely flipped over. The saucer section continued to burn, completely unsalvageable as Krall's forces combed the devastated starship, unable to locate the Abronath.
Eventually, Kirk and Chekov stumbled upon a trap set by an alien woman named Jaylah. This resulted in their reunion with Scott, who had been brought to a long-crashed Earth/Federation starship, the USS Franklin, after Jaylah learned that he was an engineer. Soon after, they were able to rescue McCoy and an injured Spock; McCoy, having finally gained access to proper medical supplies, was able to treat Spock's injury. The reunited officers and Jaylah were eventually able to mount a rescue of the captured crew. Moments after the rescue, they were forced to launch the Franklin, by now spaceworthy, from Altamid and fly it to Starbase Yorktown, which was under attack by Krall.
With the destruction of the Enterprise and the subsequent defeat of Krall, a Constitution-class starship already under construction at Starbase Yorktown was registered as the NCC-1701-A Enterprise and Kirk and his crew resumed their five-year mission. (Star Trek Beyond)