Eden, or the Garden of Eden, was a location controlled by the members of the First Civilization. There, they held many of their creations, humanity, who they used as a docile workforce and enslaved through technology later known as the Pieces of Eden.
Adam and Eve were believed to have been the first humans capable of resisting the power of the Pieces, presumably because they were devoid of the neurotransmitters that the First Civilization had implanted into their creations. The two were known to have escaped Eden through freerunning, after having stolen one of the Apples of Eden.
In modern times, Clay Kaczmarek, a descendant of Adam, revealed Adam and Eve's escape to his successor in the Animus Project, Desmond Miles, through a video file named the Truth; this video showed glimpses of Eden.
Later on, after Desmond had recovered all of the glyphs and solved the rifts in the Animus' programming, he encountered an executable file dubbed "the Miracle" by Clay. Through loading it in the Animus Virtual Training Program and discovering the path to navigate, Desmond encountered Clay's virtual copy, who told him "Eden. She... in Eden. Find Eve. The key. Her DNA...", referencing the location.