Throughout the game, Isaac stumbles across a conspiracy involving the Church of Unitology, the government and a realm of possibilities. Clarke is also trying to find his girlfriend, Nicole, a senior medical officer assigned to the ship, whose fate is unknown at the start of the game. Unfortunately for them, they are thrust into the middle of the nightmare that the Ishimura has become. Isaac is a ship system specialist and an engineer traveling aboard the shuttle USG Kellion to investigate and repair the USG Ishimura, accompanied by three security personnel and a computer specialist.

Isaac Clarke - The protagonist of the game.

However, the events that took place during this planet crack are the events that threatened the very survival of mankind. By the time of the game, the Ishimura performed 34 successful planetcracks and is now in the process of beginning its 35th. Thanks to planetcracking, mankind was now thriving again and resources are plentiful.

Even though there are subsequent Planetcrackers (a small fleet now existed), the Ishimura remained the iconic symbol of mankind's will to survive, even after all of these decades. The Ishimura's job was to mine other planets for their most rare and most valuable resources to take them back to Earth. The USG Ishimura was a ship designed for the new resource-gathering practice: planetcracking. At a time of near-desperation, the CEC engineered the ship that would eventually save all of humanity: the USG Ishimura.

That is where the Concordance Extraction Corporation came in. The remaining humans realized that the only way to gain the resources to survive would be to search new planets for resources. Earth has gone through an extinction-level event, caused by rapacious and unsustainable use of resources.

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