Setting
The game is set in the distant future, in which humanity's technological growth and research has led to FTL travel, the creation of colonies, advanced combat drones for space warfare, and exploration of star systems through jump gates that form a network known as the "Tal-Seto network". In the 22nd century, the United Nations (UN) has evolved from a diplomatic organization to a political group that form the laws and rules for humanity, rather than the planet's many sovereign states. However, a growing fear of uncontrolled technological development and the resulting possibility of the creation of artificial life, leads to the UN instigating harsh, extreme laws to restrict technological development and research to preserve human life. In response, several nations, including the United States, and various colonies beyond Earth secede from the UN and form a military political coalition called "The Alliance", with a belief that technological development, and the possible deaths it can cause, far outweighs the restrictions on freedom imposed on humanity.
The resulting split leads to a conflict between the UN, having greater production capabilities, and the Alliance, who holds its own with advanced technologies, which has lasted for two decades and devolved into a war of attrition. In the game's present, the Alliance has recently discovered alien ruins on a planet in the Deneb Kaitos system, nicknamed Persephone, after a recon drone returned from the system earlier than scheduled with the discovery. Believing that these ruins can help the Alliance win the war against the UN, a secret scientific expedition is organized by the Alliance Interstellar Space Operations Command (AISOC), consisting of ships from the United States Navy's space fleet, which is sent to the planet to explore it, find the ruins, and locate any alien technology within that can help them achieve victory.
Plot
A secret scientific expedition consisting of two ships from the Alliance - the USN SV Jericho , an unarmed science ship; and its escort, the light cruiser USS Lexington - arrive in orbit above the planet Persephone in the Deneb Kaitos system. Before the Jericho can prepare to send a lander vessel to the surface to explore it, an UN cruiser, the UNS Dharma , ambushes the vessels, damaging the Lexington in the process. The Lexington's captain, Stephen R. Dayna, offers his surrender of the crews from both ships to the Dharma, which accepts them. As the crew prepare to abandon ship, Dayna informs his executive officer, Jennifer Tran, that he intends to have one crew member be left behind in hopes they can complete the expedition's mission. After the pair chose one member (the player), Tran leave messages for them to receive when they recover consciousness, before leading a warhead onto the ship's inter-ship shuttle. When the shuttles carrying the crews from the Lexington and the Jericho are taken aboard the Dharma, the warhead detonates, destroy the ship and everyone aboard.
Moments after regaining consciousness, the player finds themselves having to repair the ship, finding instructions from Tran on the main systems to fix. After dealing with a hull breach, the player works to restore coolant to the ship's reactor and fix the central computer, whereupon a further message from Tran instructs the player to contact the Alliance at their colony on the planet Erebus. In doing so, the player makes contact with Fleet Admiral Charles Decker, who is shocked to learn of what happened. Revealing that the UN are sending more ships to the star system, and advises the player to order the Lexington's main computer to move the two vessels to safety. The player obeys (triggering a bad ending), or refuses and chooses to follow Dayna's wishes for them to complete the mission. Decker attempts to reason with the player and reveals the expedition was being conducted in secret to find alien ruins on the planet that a recon drone discovered, when it explored Deneb Kaitos, in hopes of finding technology to help the Alliance win its war with the UN, relunctantly admitting the war is going badly.
The player, despite this knowledge, refuses to give up, and learns from Decker that the UN ships could be defeated through the use of an experimental chemical enhancer aboard the Lexington called "HYPE", which allows the user to be able to micromanage combat drones in space combat more efficiently than normal humans can due to the speed of space battles; however, the user will suffer serious side effects in time that eventually lead to death. With this knowledge, the player proceeds with their mission by bringing the lander from the Jericho to the Lexington, preparing it for the descent to the surface, and then using a syrum of HYPE in order to defend the vessels from the UN. When the lander is ready, the player ventures to the surface, and finds the ruins. Inside, he uncovers technology that allows him to form machinery reconstructed from metal scattered around the ruins and surface, which in turn build a time gate. Choosing to venture into it, the player finds themselves brought to Earth in the future, in has been devastated in an even greater war. Seeking answers, the player comes across artificial life known as ELFs - electronic lifeforms
The ELFs reveal to the player that in the future he is one where the UN achieved victory and implemented a restriction on the creation of AIs on all known worlds. However, decades after the war, a group of underground scientists created ELFs in a remote outpost, and the UN's efforts to destroy these resulted in the ELFs waging a war that plunged humanity to the brink of extinction. The player learns that in order to win their war, the UN used a weapon of mass destruction to destroy the Tal-Seto network, while sending the surviving humans out of the galaxy on a ship with new engine drives. The ELFs reveal that because of the weapon, the galaxy and everything in it is now on the verge of destruction. Using a special program, the ELFs reveal how they intend to send the player's consciousness back into the past before the attack by the Dharma, in the hopes they can change history and prevent the unfolding disaster in this timeline.
The player agrees, and returns to the past, where they soon find themselves restrained by Tran over his sudden, erratic behaviour. After the player incapitates her, they swiftly acquire HYPE and inject themselves with it, before heading to the bridge, warning Dayna of the imminent attack. Despite suspicions and his anger at the player using HYPE, Dayna reluctantly lets them take charge of the ship's drones when the Dharma is located. The player manages to destroy the Dharma, and swiftly assists the Lexington and Jericho in finding the alien ruins. Recreating the same steps that led to the creation of the time gate, the player uses it and heads to the future.
Once there, the player discovers that with history changed, the Alliance won against the UN, ending its laws on technological development. In time, humanity created ELFs, which were welcomed as equals. As a result, Earth was abandoned after the ELFs created a new home for them all - a large dyson sphere surrounding the sun, with the interior populated by humans, and the exterior by ELFs who would grow to explore the facets of the multiverse outside the realm of human understanding. The game ends with the player contemplating the meaning of human existence, and questioning the fate of their alternative self in the previous timeline.
