Disclaimer: I am not a troll. This is a plausible theory that I have developed over time. There is no TL;DR. Please read before commenting and remember: "You have no rights, so play nice!" -Bungie.
One of the least occurring thoughts when you hear the word Halo is PlayStation. After reading this, you may change your mind. I'm not a big fan of the PlayStation, but as a kid all I had was a PS2. Some of the games I would enjoy playing were Ratchet and Clank, Jak and Daxter and Grand Theft Auto. Take a moment to pause at the name Jak and Daxter, what comes to mind? It was made by Naughty Dog, a company all itself. If you don't know the story of Jak and Daxter, don't fret. This theory should fill the gaps.
Before we get down and dirty, I will have you know that Jak X Racing and Jak and Daxter: the Lost Frontier are not part of the real Jak and Daxter storyline because A) One of them's a racing game and B) The other was made by a different company to get money. Also before you can sit down and untangle those reading glasses, Jak and Daxter is the second most amazing game of it's time (under Halo: C.E.) with amazing graphics, gameplay and storyline concept as well as strong pacing. It is not a kid's video game and should not be treated as so.
The intro to the first game is here.
To start off, we know that the Precursors created derelict monoliths to give that planet it's "energy". Dark Eco, Red Eco, Yellow Eco, Blue Eco and Green Eco as well as the famed Light Eco. Now, just because the Precursors are called precursors doesn't mean they're the Precursors of the Halo Universe, but I can still find evidence.
This world seems to be so fresh, that energy within it is malleable. (like in Avatar: the Last Air Bender) Dark Eco, like what you saw in the intro, heavily mutates the body. This can also be a theory as to how the Flood originated. All this time, Jak was born in the Future and sent to live peacefully in the past. It's weird how these tribes people can manipulate Precursor tech, which reminds me of how an enlightened civilization of super-hermits live.
The Covenant also has an obsession with the color purple. Lurkers are purple, but in this theory, Lurkers did something to make the Prophet species worship them, thus demanding that the Covenant fly with purple colors. This is because Lurkers look nothing like any Covenant species, so they must be Gods. Jak and Daxter have long, elf-like ears. This suggests that they are A) The form of Humans that existed before the Galaxy was wiped out or B) Forerunners. Something leads me to believe, though, that they are ancestors of Humans because in Jak 2 and #3, Haven City is similar to the industrial style of Modern Man today.
The planet that Jak once inhabited, if this theory is true, will soon be wiped out. It could be for several reasons, some being that the world was engulfed in Dark Eco, destroyed by the Ring World and/or taken by the Flood. If malleable energy existed on this world at the period, then it existed on others as well. The Flood is evil, tainted and impure, something that only Dark Eco could create.
There's no way that Jak and Daxter being eerily similar to Halo is a coincidence.
In conclusion, even if Jak and Daxter have nothing to do with the Halo Universe, I personally hope it does because it would add more meat to the saga's history. Fin.
[Edited on 01.26.2011 5:33 PM PST]