Hi,
There are a lot of theories out there without real evidence about how Marlton is a time travelling scientist from the future to save us, or how he's some huge traitor siding with Rhichtofen. I've recently found something that finally proves that it's all a load of bull.
So I was on callofduty.com, and decided to look at information about the BOII Season Pass, and found an interesting description of Nuketown. (link: http://www.callofduty.com/blackops2/dlc/seasonpass )If you don't feel like going there, it says at one point:
"A group of radiation scientists are investigating the Nuketown remains and discover soldiers that have been revived by Element 115 from a nearby Nevada base. The zombie soldiers attack the radiation scientists and turn them, and after receiving a distress signal, the base in Nevada sends in CIA and CDC agents to investigate."
Ok, HUGE story explainer right there. The theory I get from this is as follows:
Marlton was with those radiation scientists working at Area 51, and was doing experiments with 115 before he became trapped in the Nuketown Fallout Shelter. Sort of like an American Rhictofen, but without a personal vendetta against guy like Maxis. He was with the scientists we hear the radio transmissions through the TV at Farm from at Nuketown, (edit: Jackass Flats. Thanks @charries96.) proved by when you hear the coordinates. They had started hearing Rhictofen and Maxis giving orders, telling them to bring each other down. The scientists became torn and started fighting. Zombies came, and a Grief match of sorts arose. In the end, they all were turned except for Marlton, who had picked no side. (edit: see update.) They exiled him for this, shown in the quote heard from him in the shelter: "...abandoning someone for being different..."and he hid in the fallout shelter for safety. All scientists were killed, and the CIA/CDC came.
Now for my lesser proved theory.
You know how you hear T.E.D.D.'s horn go off near Nuketown? I think that the original route he was supposed to take passed near it. When T.E.D.D. passes the blocked road next to the diner, he says:
"Error, error. Global Positioning Navigation Error. Continuing current automatic rerouting system." or something on the lines of that.
This shows that T.E.D.D. could have been on an original route by Nuketown, and instead was looped back into Green Run. Perhaps Marlton followed T.E.D.D. on the bike (edit: It's more probable that he ditched the bike and jumped on T.E.D.D.'s bus. That would explain how he made it so far, and we see no bike in Green Run. Thanks @Infest and everyone else who pointed it out.) or something like it to get to the bus station? This part is unconfirmed, and I really would like to hear your theories. Please just add reason to why you think you know what's happened. We, as the community, don't need any more nonsense theories or trolls out there.
Good luck! Hopefully we can get to the bottom of this!
UPDATE:
First, something small that I didn't include in the OP. I think that the scientists at Jackass Flats never had actually went to Nuketown. The zombies are the ones who had actually put on the equipment to stay safe from the radiation and go out there to get samples, whereas Marlton and everyone else there were the people that studied it.
Next:
oM Blitz really changed my mind and summarized the bottom half of the story perfectly. It's more likely that all of the scientists at Jackass Flats (excluding Marlton) consumed the Flesh, not just half and half. Speaking of the Flesh, I believe that everyone in it are the people that have a direct mental link to Richtofen. Something with the 115 in the body makes me think it must have some effect on the body, and it would explain why Samuel is the only one who can hear Richtofen outside of the drops. As per something I had recently read on another thread, (sorry for not citing who, can't remember off the top of my head,) perhaps the drops have a direct link to the Aether, and sense Marlton didn't eat/join the Flesh, he can only hear Richtofen during the effects of the drops.