I have been tossing around a theory on this for awhile and something similar (which I will not give away due to those who read my stories and Spartan 626 as I do not wish to spoil) to what many of you have said but, in the opposite direction. Bare with me while I explain:
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We know that Spark lost contact with Penitent Tangent 3,000 (approx) years after his previous (and final) communication which would would put their last contact at about +1500 years after ring activation.
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This means that 4,575 years after the rings were activated (In other words, about 100,000 years before humanity would land on Installation 04), Guilty Spark had no communication with his fellow monitors and, most importantly in this case, Penitent Tangent.
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We also know that the final communications from Penitent Tangent were “incomplete and quite perplexing” but he never goes into much detail.
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We know that there was a ship that crashed on Installation 04 at (approx) +60,000 years after ring activation.
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Ironically, Guilty Spark was never able to identify any remains and/or anything (at all) from the occupants of the crashed ship. It was as if the ship just randomly crashed without any occupants but with a looping distress signal. Surely Installation 04’s Sentinels would have found remains of anything on that ship. However, from what Spark states, there simply wasn’t anything to go by.
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In regards to the previous entry. It should be noted that the ship burned up on its crash. Likely the fire incinerated everything inside the hull.
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The ship bares a resemblance (to me at least) of the ships from the Forerunner vs Ancient Human space naval battles. More specifically, if you watch the Halo 4 terminal videos, watch the first entry (before the Librarian begins speaking). To me, the ship that landed has the same design (yet smaller) as the Ancient Human flood infested ship that the Forerunners destroy on the first Terminal entry.
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We know that Ancient Humanity and the Forerunners were both, at one point or another, at war with the Flood.
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We know that the Flood was extremely widespread by the time of the Halo Activation. They had the Forerunners boxed in and were it not for the Halo Rings and Offensive Bias giving them time, the Flood would have swept the board clean.
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The Halo rings eradicated the flood… except for the Flood samples in containment.
What my theories currently are:
a) We must assume that, like Installation 04, the same samples were contained on each installation. This would be logical as it would assure that research could continue on numerous entry points at once instead of depending on just one or a few.
b) The Gravemind on Installation 05 had intricate knowledge of Forerunner technology (as seen by its ability to teleport two organics to two locations that were across space - a massive feat in itself).
c) The Gravemind on Installation 05 (as seen in Halo 3) had intricate knowledge of humanity and their relation with the Forerunners (“child of my enemy why have you come, etc”). This adds to one of my oldest speculations that Graveminds are connected regardless of death because each single flood spore contains the entire genetic makeup for the Flood. It’s memories, it’s history, it’s knowledge base, and it’s ability to use and repair an assortment of technology. An example are normal flood forms being able to drive vehicles or use weapons. The forms all fall under the Gravemind, yes, but they all maintain the knowledge base because they all possess the same genetic structure from the spores themselves. In other words, if a Gravemind is destroyed, existing Flood forms (if infection is widespread enough) can come together and quickly form another for coordination and the hive mind leadership required for the Flood to expand.
d) Why are the above two important outside of the revelation given? Because if I am correct then that also means that the Flood, given their true origins, are also able to use neural physics, star roads and, most importantly and according to Bornstellar, Unbending Filaments which linked worlds and systems. Only one other race used this technology, Ancient Humans. My point is that it is extremely feasible and extremely logical to speculate that in the 60,000 years between Penitent Tangent going dark, that during the issue(s) on 05, the Gravemind there found a way, by using technology found on the ring, to reconstruct transport off ring which, in my view, is the very vessel that crash landed on 04 all those years after Penitent Tangent went down.
e) In other words, I believe that Penitent Tangent’s negligence began the chain reaction which led to not only the Gravemind being formed but also the ship hitting 04 and, at this point, perhaps other issues such as Onyx’ latent flood and other information we have (Flood in Halo wars for example). Simply stated, Installation 05 was a staging point by the Gravemind, which was not yet a Gravemind but, rather, genetic material coming together to form a Proto-Gravemind based on the broken containment spores and flood forms that also broke free, which used its vast knowledge base to create and to send the very limited resources it had out to various areas which pulled organic material and brought it back to Installation 05 which helped create the super form. With its ability to teleport and its knowledge of neural physics, this is a feasible conclusion in my eyes.
Very long story short, Penitent Tangent’s inability to monitor and maintain containment, mixed with the Floods ability to adapt, mixed with the resources available on Halo Rings, mixed with the Floods timeless knowledge of technology, mixed with the plentiful, yet (at that time) unknown locations of organics allowed the Flood to assimilate species they found while also allowing it to prepare for the events we end up seeing in Halo 2 and beyond.
Thanks for the read folks. See you soon in H2!