The team thus decides that they have to find a shuttle and escape while they can. Clarke and Hammond subsequently recover the Valor's power center in order to repair an shuttle, but Hammond is killed by a Necromorph from the process. The living Dr. Kyne later contacts Clarke and urges him to return the Marker to Aegis VII. He shows in a movie what the planetcrack caused: a large creature called The Hive Mind, the creature that controls all of the Necromorphs, was permitted to escape the minute the world was cracked, and started infecting the colony. He considers that the Marker actually acted as an inhibitor, making the Hive Mind dormant as long as the Marker remained in the world; the Hive Mind's dormancy would also lead to the rest of the Necromorphs to enter a dormant state. He concludes that the only way to prevent the creatures for good would be to return The Marker into the planet.
Clarke takes the shuttle with the Marker to the colony, and replaces it there; this pacifies the Hive Mind temporarily, but also disrupts the gravity tethers holding a large portion of the planet several miles off the surface, threatening to destroy the colony. As Clarke attempts to escape, Daniels looks and takes the Marker back to the shuttle, once again removing the 'dead space'-area pacifying the Hive Mind, and shows Clarke that Nicole really committed suicide before they came on the Ishimura, and Clarke's dreams of her was the Marker's way of attempting to bring itself back into the planet, revealing that it's sentient somehow. Before she can leave, Daniels is killed by the colossal Hive Mind, but Clarke is able to defeat it. Leaving the Marker behind, Clarke flies off in the shuttle just before the rock crashes into the planet, ravaging the surface of Aegis VII.
The newly created infection escaped and started to kill the physicians and change them, and it wasn't long before the colony dropped, but the doctors were successful in editing the Marker to an inhibitor of the disease, and activating this new feature. With the doctors dead and the disease locked away, the government marked Aegis VII as off-limits and abandoned the planet. The planet cracking operation was actually a mission by CEC and the government to retrieve the valuable mark, which led up to the present events. She then leaves on the shuttle without Clarke, but Nicole arrives and is able to help him recall it, prompting Daniels to flee through an escape pod.
After being assisted by Clarke in loading the Marker on the shuttle, Kyne is murdered by Daniels, who reveals the truth behind everything: she is a government operative ordered to retrieve the Marker for her superiors. She further reveals that the Marker is a reverse-engineered copy of another Marker found on Earth, and has been placed on Aegis VII from the government tens of thousands of years ago to have scientists study its effects. These scientists discovered the pattern covering the surface of the Marker is, in actuality, that the DNA code for Necromorph infection.
Dr. Kyne did not seem to wish to kill the captain, and the death may have been a freak accident, but it may also have been a momentary loss of control as the existence of the Marker on the ship has been causing the same homicidal paranoia as was experienced on the colony. The infection then spreads to the Ishimura via a colony shuttle piloted by a survivor, who was unaware that a Necromorph had entered his shuttle prior to take off. The shuttle crashes into the docking bay, allowing the creatures to escape in the Ishimura ventilation system and start killing and infecting the Ishimura's inhabitants. Shortly thereafter, all of the emergency shuttles and escape pods of the Ishimura are launched -all of them empty.
Shortly after the Marker was extracted and brought into the Ishimura, a huge section of the civilians -first on the planet-side colony, then on the boat -suffered from intense hysteria and paranoia brought on by violent hallucinations. The health care teams in each area screened for diseases and distributed sedatives, but the agitation of the team could not be contained for long and the outbreak of paranoia evolved into mass homicidal and suicidal impulses. These phenomena were believed to be linked to proximity to the Marker, but the colonists had no idea how or why it was happening.
The Church of Unitology and the ship's captain then quickly replaced or won over many of the ranking officers of their Ishimura. With the upper echelon of the ship in Unitologist hands and the records of the mining operation made confidential because of the Aegis VII quarantine, the Unitologists had the perfect opportunity to capture the markers and use it to discover the secrets of human formation, development, and purpose they believed it contained.