Prior to the battle began, Zuka 'Zamamee formulated a plan to eliminate John-117. His Grunt offsider, Yayap, was left to be found by the UNSC forces, and transported to Alpha Base. Once he spotted John-117, he activated a signaling device to call in Zuka's attack force. However, by the time the battle had started, John-117 was well on his way to the Installation 04 Control Room.
The Battle for Alpha Base began with a distress relay call from the Pelican dropship Charlie 217. This Pelican had been listed as MIA, but was allowed to land on one of the pads at Alpha Base, although an ODST reaction force was put on standby. The Pelican was piloted by LieutenantRick Hale, a Covenant prisoner. As soon as the Pelican was given permission to land, the Lieutenant was then strangled to death by Zuka 'Zamamee using an Energy Garrote. 'Zamamee then landed the dropship by himself. Wellsley, however, read the thermal readings given off by six Covenant dropships crossing Alpha Base's perimeter and was about to warn his superiors. However, Charlie 217 had already landed, and the battle thus began.
Thirty heavily armed Stealth Elites disembarked from the dropship and attacked every human in sight. Despite being caught fully unaware, the UNSC forces rallied and fought back well, setting fire to the pad Charlie 217 landed on, killing many of the opposing Elites and destroying the Covenant-captured Pelican. However, Major Silva now had to deal with the problem of preventing all of his remaining Pelicans from roasting in the fire.
By this point, the 6 Spirit dropships were spotted heading for Alpha Base at 350 kph by the Alpha Base A.I., Wellsley. Wellsley utilized a 50mm Autocannon and shot down one of the dropships before they could get past it. The 5 remaining Covenant ships, unable to land on the base's landing pads as planned, touched down on the mesa and unloaded the main attack force, led by Field MasterNoga 'Putumee. Meanwhile, Zuka 'Zamamee and five of the remaining Stealth Elites descended into the underground level of the base, slaughtering all the humans that they came across. Finally, they entered the Control Room and massacred Cho, Pauley, and Mary Murphy. However, they were seen by Wellsley, who promptly warned Silva. Soon, six teams of 3 Marines were set out to halt the Stealth Elites; to counter the active camouflage, the Marines had special items which allowed them to read the thermal heat given off by the active camo. The Elites questioned everyone they came across in an attempt to learn John-117's whereabouts. Eventually they came across Yayap and three other Grunts in a prison cell. The Grunt convinced Zuka that the Spartan was guarding a group of captured Banshees on the other side of the base, and led the group toward there. A 3-man Marine fireteam surprised them, killing the five Stealth Elites and the three Grunts before being taken out by a plasma grenade from Yayap. Knowing that the battle was lost, Yayap forced 'Zamamee to fly them out of the base upon reaching the Banshees.
Meanwhile, on the plateau, McKay was in command in halting the Covenant forces. First, the snipers attempted to kill the majority of the enemy ground forces. 'Putumee, unable to land on the pads as originally planned, alternatively landed on the area up-spin of the Forerunner complex. Despite having the remaining Spirit dropships strafing the Marine defenders, they were caught unaware by the pair of entrenched Scorpion Tanks and prepared defenses on the plateau. Although 'Putumee did notice that the trenches were too neat to have been dug in response to his assault, the thought crossed his mind too late. Not only did the Scorpions obliterate the majority of the Covenant forces, but also deprived the Covenant forces of their leadership when 'Putumee was killed. However, the assault moved onward, albeit slowly, as the lower-ranked Elites assumed command and attempted to rally the troops with little success. The strafing Spirits picked up the few surviving Covenant troops and retreated. The Battle for Alpha Base was over, ending in a UNSC Marine Corps victory.