Now tht Reapers have been defeated and they are making ME4, Protheans should return after 50.000 years and try to conquer the galaxy. Turns out that Reapers needed to harvest people because they needed the resources to fight the Proteans of, and with Reapers gone Protheans are coming....
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Applied Science? All science is applied. Eventually.
Nah, I'll pass. That's pretty much the plot of Halo 4, and it's fairly well laid out how the Reapers mopped the floor with the Protheans in the span of the ME games. Javik explains it in pretty explicit detail.
shareThe Protheans are the Collectors. The only remaining Prothean is Javik. And some of the remaining Collectors have "awakened" from their servitude state and are now fighting alongside the N7 special forces in the ME3 multiplayer.
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Technically they already were antagonists, with the Protheans being the Collectors.
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