: I don't know what you're talking about, and I probably won't for a long time
: since I don't have a copy of Halo 2 on me and I don't exactly intend to
: play it the instant I finish Halo:CE.
: Marathon Logos mean their religion is bogus...? Is it because it's a sign
: that some other species achieved space travel? The thing is, the Marathon
: canon obviously doesn't exist in this universe, so I really don't know
: what Marathon logos are doing there or what it means.
The Marathon logo in Halo is the Forerunner glyph for "Reclaimer" meaning humans. By reading the glyph upside down, the covenant misinterpreted it as "reclamation", thinking that they could recover precious Forerunner artifacts they couldn't find elsewhere, upgrading their technology.
A covenant Luminary scanner picked up the humans on Harvest and tagged them with Marathon glyphs. Mendicant Bias in High Charity's forerunner dreadnaught revealed to the Halo 2/3 prophets that the glyphs meant humans, that humans would take the Forerunners' "mantle" and that the Covenant were meddling kids.
The prophets ordered the extermination of humanity to prevent the rest of the Covenant from finding out the truth as their religion was the only thing that kept them all together.