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Author's note.
I felt that I had to tell the story of what happened to the Flood before we arrive on Halo. If I didn't do this, the way I plan on making the story wouldn't make sense. I'll send in the first part on the Flood's point of view shortly.
Deep inside the many crevasses of Installations 01-10, Flood samples were kept under high watch. The walls of their prisons were made specially by the Forerunners to prevent escape. Knowing the great danger and great importance of the Flood, they were kept for future study. Special guards were created to maintain the Flood and to make sure they didn't escape. The Forerunners were not unwise in keeping the Flood, as they knew of the importance they possessed. The Flood were the basic forms of bacteria-viruses. They were the missing link, the equivalence to "Big-Foot" in human evolution.
The Forerunners discovered these creatures deep within the core of their home world. Once discovered, the Forerunners decided to take live specimens for future study. It was soon discovered that the Flood were trapped within the core, in hibernation, and that they were very dangerous. The Forerunners had to develop special weapons in order to combat these creatures because as it turned out, they had the ability to overtake even advanced species. This was not a problem for the Forerunners however. Being so technologically advanced, they eventually created a special class-12 armor, which completely prevented any Flood infection. With their new class-12 armor, all the Flood could do was watch as they were taken away from their world and brought to the surface. The Forerunners marveled at their new discovery. They studied and gathered as much information as they could.
Then the day came, and the Flood escaped. The people in the Forerunner's cities, lacking the combat armor, fell victim to the Flood. Nearly 1/3 of the planet's population was infected before the class-12 armor was created in mass production for everyone's protection. The problem was that the Flood took control of all of the motor functions in their victims. The Forerunners had little choice but to kill each and every one of the infected people. Focused on never having this happen again, the Forerunners had some serious decisions to make. They could either destroy all of them, or, they could find some way of containing the Flood for future study.
Thus, Installations 01-10 were created. The installations were ring shaped constructs that had oxygen-nitrogen atmospheres, were 10,000 kilometers in diameter and 22.3 kilometers thick. They had gravity fields that controlled the ring's spin and kept the atmosphere inside. The ring shape was the easiest shape to construct because a large sphere was too broad and didn't give the control that the Forerunners needed. The design was also perfect for all the installations the Forerunners planned on having within the ring.
The other installations were made for research but Installation 04 would become a zoo of sorts for all of the Forerunners. Deep underground, the Forerunners placed cages in which to hold the Flood "infectious forms." Here, they would be taken away and brought to the surface for study and analysis. The Forerunners wanted to see how each environment affected the Flood. The Forerunners believed that these Flood might have very well been the last in the universe. The Forerunners needed to study them; their survival as a race was dependant upon it. They created swamps, rivers, lakes, fog, and other variable weather patterns and geographical landforms they could think of. They would test out each of the Flood with great ease from the assistance their class-12 armor gave them. When they were not being tested, Forerunners could go to specific holding facilities where the Flood were kept. They could observe each creature from a very safe distance and with specially designed walls between them and the Flood. The ability for civilians to observe the Flood was the only thing that made Installation 04 unique.
The problem was that the Flood needed a host body to survive. Although they could go into hibernation for very extended periods of time, they would need a host or all of the Flood specimens would eventually die. The Forerunners developed a special gas that would freeze and preserve the Flood. Vents were placed through the holding facilities to keep a constant supply of the gas for the Flood. The class-12 armor protected the Forerunners from the gas because the suit easily filtered it out.
Throughout Installations 01-10, teleportation grids were installed for easy travel. The installations were also constantly supplying energy for those with the knowledge to tap into it because the Forerunner's armor was in regular need of it. Although the other suits had power packs within them, they were cumbersome and heavy. Scientists were able to carry more supplies and move more freely if they took the energy from the installation itself.
No one had been to any of the installations in a long time since no new developments had been made. One day, a ship full of scientists landed on Installation 07 for more research. Unaware to the scientists, the installation had one small problem. Over the years, the power grid produced an unimaginable amount of power. The power generators were designed to cool themselves so that another coolant was unnecessary. Unfortunately, the power generators did produce a very minute amount of waste heat. It raised in temperature about 1 degree every decade. Since the power generators were constantly running, over time, they reached critical levels and shut down. Now that the scientists were unprotected, the Flood made their move. They easily infected the unprotected scientists. When they realized what was going on, one scientist managed to send for help. Before the help could arrive, however, the Flood learned how to drive their ship, and headed for the Forerunner home world in search for food.
The ship was blown into a million pieces before it came within the planet's atmosphere. The Forerunners were faced with the same decision. They could self-destruct all the installations, killing off the Flood specie and end the threat once and for all. Their desire to keep this missing link, this piece of evolutionary marvel, didn't allow them to do that. Instead, the Forerunners fixed the power generators heat by placing a few structures scattered around the installation that would shoot the waist heat out into the sky. In addition to that, the Forerunners also decided to make a new form of security.
No Forerunner was allowed to freely go back and forth inside the installations. Instead, special A.I.'s were built to watch over the Flood. One A.I. would monitor each installation for research and security. They would do this in the installation's control room. In the control room, displays told the monitor everything from what was going on in the Flood's holding cells to the rotation of the installation itself. Special machines were also created. These "sentinels" would help in the research of the Flood. Armed with a special surgical laser, they could dissect each "infectious form" and do other menial duties. Progress reports would be sent to the Forerunners if any new developments occurred.
A last resort fail-safe device was also put in the installations. This "doomsday device," which had a maximum affective radius of 25,000 Light Years, would rid the galaxy of all sentient life that had enough biomass and cognitive capabilities to sustain the Flood. The Forerunners didn't know of any other specie that could hold off against the Flood. If the Flood found enough food, they would be able to take them over as well. The Forerunners couldn't let that happen and so decided that this was the best way to stop the threat of the Flood. The "doomsday device" wouldn't affect the Forerunners however because all their home worlds were surrounded by a large shield. The Forerunners, having mastered shield technology, could easily come up with something to deflect the pulse.
As the final piece to the device was built, it began to initialize itself. Before the device could obtain the required amount of power from the power generators, a small piece was taken from the device's core and it stopped. This piece, called an "index," was given to the monitor of the installation. It would be kept in one of the holding centers of the Flood. If by some chance, the Flood managed to find a way off of any installation, a distress signal would be sent to the Forerunners. A Forerunner would come to reclaim the "index" from the monitor and reunify the "index" with the installation's core. This would subsequently restart the device.
The monitor designated to watch Installation 04 was named 343 Guilty Spark. As with the other A.I.'s, Guilty Spark had every bit of information on the Flood installed. He was made of class-12 armor and had a special language decoder. All he had to do was observe a specie and he would learn their form of communication, whether it be verbal or otherwise, with a complete understanding. This was in case another organism managed to find the installation. 343 Guilty Spark was there during the installment of the fail-safe device. During which, the Forerunner installing it asked him whether or not they were doing the right thing in not destroying the Flood. The monitor processed the question for a bit of time before he answered that he did agree with what the Forerunners were doing.
The Forerunners left the A.I.'s in charge of the installations and went back to their own world. As time passed, less and less information was sent to the Forerunners. Eventually, the Forerunners came to the conclusion that they had learned all they could about the Flood. Even so, they kept the Flood on the installations for a deep desire of keeping this piece of the past. Eventually, the Forerunners began to use all of the natural resources in their planets. One by one, each planet was abandoned in search for new inhabitable planets. When one planet was moved from, some technology was left behind, partially because it could easily be remade and partially because it was too cumbersome to take with them. Eventually there were no Forerunners left occupying the space around the installations. The Forerunners told the A.I.'s where they had moved and how to contact them in case of a need to activate the "doomsday device." Although the Forerunners would take a longer amount of time to respond to an outbreak, they were confident that nothing would happen since the installations had been around for so long, without any tribulations.
Finally, after centuries of research, the monitors on all of the installations came to the conclusion that they had gathered as much information as they could. Using the newfound research they had, the monitors told the sentinels how to create a new chemical that put the Flood in deep dormant stages. Unwilling to give the Flood hosts to survive, the monitors tried as best as they could to preserve the specie. Knowing that the Flood couldn't last forever without a host, the monitors had bought an estimated millennia for the Flood's survival. With no hosts and no way to escape, the Flood lay dormant for over a 100,000 years. Then the trespassers came, broke them free and fed them with their bodies. With food and a place to go, the Flood spread through the underground subsystems of Installation 04 looking for a way to escape.
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