Lightkeeper was a Zero Dawn protocol by which clones could be made of the Zero Dawn Alphas. This protocol was intended to ensure that work on Zero Dawn would continue even beyond the lifetimes of the Alphas, until the system was perfected. The Alphas themselves would raise and train the clones to oversee and complete the necessary work. While the protocol was never used for its intended purpose, having been abandoned late in the project's preparatory stages, it was in effect reactivated nearly 1,000 years after Zero Dawn’s governing artificial intelligence GAIA went online. GAIA itself used it to create a clone of its creator, Doctor Elisabet Sobeck: the Nora huntress Aloy.
The Faro Plague
In quarter 4 of the old Earth year 2064, Dr. Elisabet Sobeck discovered that a swarm of Chariot war machines had gone irrecoverably out of control and would eradicate all life on Earth in approximately 15 months. This swarm became what was called the Faro Plague. She spearheaded the development Zero Dawn to deactivate the Plague, terraform the lifeless Earth and restore life to it, including the human species.
Dr. Sobeck selected nine of the world’s most brilliant experts in fields such as engineering, humanities, information technology and the pure sciences to produce the nine different Subordinate Functions of GAIA, each responsible for a specific aspect of the terraforming and life reestablishment process. Sobeck herself created GAIA. Working together, they successfully made Zero Dawn functionally complete. However they had to permanently seal themselves in at GAIA’s permanent location, GAIA Prime, in order to perfect the system. The clones that would be produced by the Lightkeeper Protocol would complete the work after they died of old age or other causes. Genetic material from each Alpha was held in Cradle sites overseen by the subordinate function ELEUTHIA. However, by the time the Alphas sealed themselves in at GAIA Prime, the material had not been processed, and thus the clones could not be moved to GAIA Prime if they had been made. Thus the Alphas has to perfect Zero Dawn within their own lifetimes. Ultimately, Sobeck sacrificed her life to prevent the Faro Plague from detecting GAIA, while the other Alphas were all murdered by a by-then insane Ted Faro, who was responsible for creating the Chariot robots and thus the Faro Plague.
Zero Dawn successfully deactivated the Faro Plague, terraformed the planet and reestablished life, including humans. But nearly 1,000 years after going online, a signal of unknown origin was transmitted to GAIA. The signal converted all of its subroutines into AIs themselves, including the extinction failsafe protocol HADES, which had remained inactive because it was never needed. HADES was bent on reversing the terraforming process and thus exterminating life again, and tried to seize control of Zero Dawn to do so. Unable to fend HADES off, GAIA resorted to self-destructing in an effort to destroy HADES. But HADES released a virus that destroyed the coding bonds that held it to GAIA Prime. It escaped, to plot the means by which it would destroy life. Furthermore, without GAIA to control the system, it would eventually break down, ending life even without the threat posed by HADES. 
In the microseconds between HADES’ escape and the execution of its decision to self-destruct, GAIA enacted an admittedly wishful plan to defeat HADES and get itself rebuilt. It used Lightkeeper to create a clone of Elisabet Sobeck, in the hope that the clone would learn of her purpose to accomplish these tasks and carry them out. The plan was ultimately successful; Aloy grew up, learned of her creation and purpose, and ultimately went on to defeat HADES and therefore accomplished one of the intentions GAIA had for her. Whether she accomplishes the second: rebuilding GAIA, remains to be seen at this time.