Arcian wrote...

Update: Thanks to the story leaks, the prothean has been confirmed to be a recruitable character in the game. My theory, however, is almost universally wrong on the details around the character and how we recruit him (not a big surprise, really), but that doesn't stop it from being a possibly entertaining read. Once the game is released, I will remove the theory from this thread and make it into a standard support thread.
Most of you have heard the rumor of the prothean squadmate - probably from me, since I very rarely shut up about it. The rumor was started when the Origin site posted a content list for the N7 Collector's Edition containing a text implying we could get a character/adventure called "The Prothean". That's when the "Prothy" rumor was born.
I have reviewed almost all lore on the protheans to come up with a theory on how a living prothean might be possible. I don't think he or she was part of the Ilos group, but instead he or she is somewhere on Mars, and that said prothean was part of a secret project (much like the Conduit Project on Ilos) to protect humanity from the Reapers. They did this by studying us up close and observing our progress from their outpost on Mars. At some point, these protheans used their ships on Mars to encase the Sol Relay in a massive layer of ice, creating an ice planetoid that we would later call Charon. They did this to prevent other species - or the Reapers - from interfering.
From examining the evidence from Ilos, it is very likely that the protheans knew of the Reapers before the invasion. They started many projects to try and stop them. They also had a backup plan in case the Reapers attacked before they were ready, which involved building massive cryo-centrals below the project facilities. The team on Ilos had their cryo central in the archives, and the team on Mars had theirs below the outpost.
The team on Mars also had the benefit of having ships in their outpost. Using these ships, they refuelled the helium3 reactors powering their cryo-central roughly every 300-500 years, spending roughly 3-6 months every "cycle" mining new fuel and studying human progress. This way, they have managed to survive up to modern times.
In 2148, humans found the prothean outpost in the middle of their latest cryo cycle. Even though they remained hidden, humanity found their ships, a mass effect core and one of the data caches containing their research on the cro-magnon era. Humanity soon spread into the galaxy by discovering the Sol Relay hidden inside Charon.
While humanity as a whole focused on expanding outwards, certain elements in the newly created Alliance focused efforts on finding more prothean caches on Mars. At some point, they may have found the cryo-central below the outpost, as well as the sleeping protheans and their additional data caches. For years, they may have kept them secretly in stasis, studying them and their data - some of it containing evidence about the Reapers - to gain an edge on the galactic scene. At some point, a man named Keiji Okuda may have come across this information and stored it in his graybox.
What is also interesting is that in ME1, we receive a trinket for helping Sha'ira. When used on a prothean orb on Eletania, we receive a vision from a cro-magnon human being studied by protheans. This trinket, and the act of using it, are plot flags in ME2, even though they are not referenced there. Most likely, the trinket, the vision and the significance of the prothean observation team will be of great plot importance in ME3.
In the Firewalker DLC, we also find a prothean orb on Kopis that will possibly have an importance in ME3.
What's also interesting is that we will be visiting Mars during ME3, likely after escaping Earth. Since the only thing noteworthy on Mars is the prothean outpost, I suspect the trinket and orb from ME1 and the orb from ME2 will have an importance here.
Also, something of interest that was shown during the part between the live demo and the live Q&A in Jesse Houston's live stream of Mass Effect 3:

Maybe this is the prothean, in stasis? Sure looks like something is floating in fetal position inside the orb. Hard to say at this point, but I thought it was noteworthy enough to mention.
This Cerberus Daily News story is also noteworthy:
01/10/2011 - Scientists on Mars Assess New Chamber in Prothean Ruins
“Controversy brews tonight as scientists on Mars assess the contents of a newly opened chamber in the Prothean ruins. The opening has been a dream of exoarchaeologists for decades, delayed by the many steps necessary to replicate Prothean code keys and crack the cryptography for entry. Critics say the Milky Way Foundation, which provided supercomputers for the cryptanalysis, could hoard any Prothean discoveries. Dr. Unira T'Lam, liaison from the Citadel Committee on Paleotechnology, says she's been kept in the dark. "Foundation personnel have orchestrated a security system that keeps out everyone except a select cabal," she accuses. "Anything could be taken from inside and we'd never know." Dr. Ilsa Warren, who heads the analysis unit, dismisses the allegation. "We've made it clear all technology stays in situ throughout the cataloging and analysis process, which could take years," she says. "Dr. T'Lam's fears would be more appropriate closer to the end of the decade."”
As get fired up has noted, the Milky Way Foundation is a front for Cerberus, created in 2168 to funnel money.
I'd just like to give credit to Mimaz98 for his inspirational theory about the Prothean Legacy, and thank Mesina2 for helping me with the research.
I wanted to give thanks to Mesina2 (again) and Squee913 (known here on BSN as SpiffySquee) for making these videos about the theory (based on the longer blog version):
Prothean Squadmate Theory part 1
Prothean Squadmate Theory part 2
I also want to highlight these youtube videos by user gamermd83, which touch upon the subject in this thread (prothean squaddie) and protheans in general:
Part 1
Part 2
Part 3
Part 4
This thread will mainly serve as a discussion and support thread. If you want to support Prothy or protheans in general, feel free to join this group and/or use these banners:


For those who are interested, I've moved the longer version of the theory here.
awesome thread dude, the collector's ed. is gonna be worth evry penny!!!