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Mass Effect & Mass Effect 2
The Prothean beacon downloaded its knowledge into Lt. Commander Shepard on Eden Prime, causing confusing dreams and visions. While the imagery is becoming clearer with time, the meaning of the beacon communication remains elusive.
It has been suggested that Prothean data recording is highly dependant on a certain point of view, what Carl Jung described as the collective unconscious. The 'cipher' needed to comprehend the images implanted in Shepherd's mind is the cultural knowledge of a Prothean: the archetypes, biological instincts, and common experiences universal to the race. Since the Protheans have been dead for millennia, it may be impossible to acquire this 'cipher'.