Let's just put it out there straight and simple. Halo does not take place in the Marathon universe, or vice versa. It doesnt. Here's a few reasons.
1. Bungie said so.
2. Different dates.
3. Name of the ship is Forward Unto Dawn, not Marathon.
4. Different aliens.
5. Bungie said so.
I'm not trying to flame anyone, i just want to put it out there so i stop seeing tons of threads "OMG!1!! MARATHON=HALO!!!111"
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If you look at [url=http://www.bungie.net/Inside/content.aspx?link=HistoryOfBungie_p1]The History of Bungie[/url], you'll discover that Bungie's old game ideas show up in future games.