From Halopedia, the Halo wiki
Origins is one of the seven short films comprising the anime adaptation of the Halo universe, Halo Legends. Origins is an expansive history of the 100,000 year long franchise timeline, comprised of two parts. The story is told through the eyes of Cortana and the episode begins after the events of Halo 3.
Over 100,000 years ago, there was once a great civilization called the Forerunners. However, their empire was invaded by a parasite called the Flood. Initially, the Forerunners treated the Flood as an infestation, until it was too late. The more Forerunners assimilated by the Flood, the more intelligent the Flood became. Soon, open war was on the rise. The Forerunners were confident that their valor and technology would stop the Flood. Unfortunately, the parasite had spread too far across their empire. On the verge of defeat, the Forerunners made one last ditch attempt to eradicate the Flood from the galaxy. They constructed the seven Halo rings and used The Ark to send the rings to different parts in the galaxy. The seven rings would destroy all sentient life and Flood biomass. Once the rings were in place, the effects of the rings cleansed the galaxy of all sentient life, including Flood, in an instant.
With their enemy defeated, the Forerunners then began to repopulate the galaxy with various alien lifeforms that had been indexed, storing DNA samples, embryos and live specimens. These lifeforms were then returned to their home planets.
Things are all changed when Dr. Wallace Fujikawa and Dr. Tobias Fleming Shaw invent the Shaw-Fujikawa Translight Engine, allowing humanity to move across star systems. Colony ships, such as those of the Phoenix-class, are sent throughout the Orion arm of the Milky Way, settling on suitable planets. Even after finding new worlds with which to satisfy their greed, insurrection ensues, forcing mankind to once more fight among themselves.
In 2525, humanity is unified against a single threat for the first time in its history. The Covenant stumble upon UNSC-controlled space, and proceed to lay waste to it. Humanity was outnumbered and outmatched in terms of technology and, for decades, the Covenant slowly laid waste to its colonies.
Near the war's end, the dangerous Flood reemerges, determined to spread once again. After the Great Schism, humanity and the Covenant then work together against the common foe, which soon leads to peace between both sides. The Two sides are seen fighting together side by side against the Flood in a montage. Species who were against each other, united against this common enemy they both shared.
In one scene, the Master Chief enters a Forerunner building covered in Flood growth. A Gravemind hands him what appears to be an AI memory Core. 343 Guilty Spark then emerges and transports John to the surface of Installation 08.
The final scene shows Cortana attempting to make physical contact with John-117, before her eyes turn red with the Iris symbol, implying her descent into rampancy.