Decades before the game's storyline (i.e. the year 2134), continued progress and industrialization of the world led to massive ecological problems. Also, scientists were attempting to create self-aware AIs. Their attempts resulted in disaster, mostly due to the inquisitive nature of the AIs and the tendency of humans to overreact. Fearing that "unchecked technological development will kill off the human race," most United Nations members pass an international law placing strict limits on technological research, most notably - in AI development. Due to the extreme measures UN took to enforce the law, several nations have declared that they would rather die than be denied this freedom and created the Alliance of Free States, including United States, Canada, China, Singapore, Australia, Japan, and major off-world colonies. As the result of the Alliance seceding from the UN, the latter responded by invading the former, starting the First Secession War. After the initial period of fighting, which resulted in the complete destruction of Atlanta, Georgia, with a nuclear warhead, there came a ceasefire, while both sides were replenishing their ranks and rebuilding their war machines. At the end of the ceasefire, the war began anew and increased in intensity, spilling over into the colonies. By that point, humanity has discovered Faster-Than-Light Travel, and both sides began to look outside the Solar System for means to defeat each other. By 2134, the Alliance has determined that, due to the UN having several technological advantages over the Alliance, the war will be lost within five years.
Around this time, an unmanned Alliance probe discovered alien ruins on a faraway planet named Persephone. Fearing that the UN also has knowledge of the ruins, the Alliance hastily dispatched the unarmed science vessel SV Jericho to examine the ruins for signs of Precursor technology, which may turn the tide of the war. The light cruiser USS Lexington was assigned as an escort. On approach to Persephone, the Alliance ships were ambushed by the UN heavy cruiser UNS Dharma, destroying the Lexington's Attack Drones (the main offensive and defensive space combat weapons) and rendering it helpless. The Captain of the Lexington pretends to surrender the crews of both ships, but leaves behind an unconscious officer (the player), claiming that the officer was killed in the battle. The shuttle is rigged with a nuclear warhead, which detonates while docking with the Dharma, destroying the UN ship and killing the crews of both Alliance ships.
The game starts with the player regaining consciousness and finding himself the only one on board. The immediate tasks involve finding messages left by the captain and his Number Two, which instruct the player restore communications with Alliance Command and receive further instructions. The player also has to single-handedly repair some of the battle damage, including plugging a hole in the hull, preventing the ship's reactor from Going Critical, restarting the main computer, and repairing the communications array by taking a spacewalk. All the while, there are two unseen timers ticking away, one until more UN ships arrive to investigate the disappearance of the Dharma, and the other attached to the antimatter bomb the spy snuck aboard the ship and armed in case the Dharma lost. If the player has not managed to gain access to the Lexington's tactical systems by that time, the mission will be lost. Once the ships arrive, the player has to use top-secret Alliance Phlebotinum to defeat the enemy (the RTS portion of the game), buying him more time. After contacting Alliance Command, the player is ordered to withdraw the Lexington before more UN ships arrive. However, if the player chooses to obey that order, this results in a Nonstandard Game Over. The player must recall the lander craft from the Jericho and explore the planetary ruins in hope of finding something of use.
The game then begins to use Time Travel once the player activates a mysterious portal within the ruins. The player ends up in a post-apocalyptic world - which is revealed to be the now-decimated Earth - and find their way inside a mysterious structure containing the same kind of portal found on Persephone. Having entered the portal, the player enters an enclave of ELFs (Electronic Life Forms), who reveal what's happened: the events at Persephone are the focal point that decides the outcome of the war and the future of humanity.
The player is currently in a future where the UN won the war, resulting in a galaxy-wide anti-technology crusade; however, unbeknownst to the UN, the distant Alliance outpost on Prometheus successfully created ELFs. When the UN came to destroy the ELFs, the ELFs, who were at this point like young children still learning right from wrong, decide to match fire with fire, escalating into a new pan-galactic war. Thanks to the ELFs having a superior, geometrically-exponential capacity for learning, the UN arrives in same position the Alliance once was during its war with the UN. Unlike the Alliance, the UN is able to secretly develop and deploy a war-ending plan: send its best and brightest outside the Tal-Seto jump network towards another via a spaceship without a Tal-Seto drive, then detonating a device which will violently collapse all known Tal-Seto points in existence - leading to the Tal-Seto network's utter destruction. The ELFs, having learned too late about the UN's plans and the full consequences of their actions, decide to teach the player the nature of time travel, then sending them back in time to ensure the Lexington and the Jericho survive the initial encounter with the Dharma - thus creating a new, better future.
The player, after escaping custody of the captain's Number Two, convinces the captain to use the top-secret Alliance Phlebotinum still in his possession to destroy the Dharma, thus enabling the player to change history by telling the captain, who now believes the player's outlandish tales of time travel and electronic beings, about the ELFs. The game ends as the player finishes recording his tale in his abode on the Dyson Sphere which now encompasses the Sol system, the final parting gift of the ELFs before they left the galaxy as they evolve past the point of human recognition. While the Alliance did win the war, and the bond which formed between humanity and the ELFs brought unimaginable peace and prosperity, the player can't help but wonder what purpose humanity has in the context of the ELFs.
