After receiving a distress signal from the planet Aegis VII,the Concordance Extraction Corporation(CEC) dispatches the USG Kellion to investigate. As they attempts to dock with the Ishiguro,a malfunction occurrs with the automatic docking procedure and the Kellion is badly damaged. However,the crew lands safely and sets off to find Ishimura's crew.
Isaac Clarke,the crew's engineer,enters a separate room to access the Ishimura's damage reports. Then,an undead creatures called Necromorphs kills two of the crew members,but Isaac and the two survivors,Zach Hammond and Kendra Daniels escaped before the Kellion is destroyed.
As Isaac flashes back about his late girlfriend,Nicole Brennan,The Crew learned through the audio and video logs about the Necromorph invasion. The Ishimura's illegal mining operation on Aegis VII was meant to find the Red Marker for the Church of Unitology. The Aegis VII colony was almost wiped out by mass psychosis triggered by the Marker,causing killings and suicides. The Marker was brought aboard the Ishimura along with the survivors,including Kyne and Mercer.
Hammond is killed by the Necromorphs and Mercer allows himself to be transformed by them. Kendra kills Kyne before revealing her Earth Government allegiance,as the deranged Kyne threatened to return the Marker to the Necromorphs' controlling Hive Mind on the planet.
Reunited with Nicole,Isaac sabotages Kendra's attempt to escape the Ishimura,returns the Marker to Aegis VII,neutralizing the Necromorphs and initiating Aegis VII's collapse. Kendra retrieves the Marker and reveals to Isaac that his encounters with Nicole were hallucinations created by the Marker to return it to the Hive Mind. Kendra is killed by the awoken Hive Mind before she can escape with the Marker. After killing the Hive Mind,Isaac leaves on Kendra's shuttle as both Aegis VII and the Marker are destroyed. Isaac relaxes as he flies into the stars.