Okay, so in Nobledark Imperium, The Emperor is last remainying of the Man of Gold, a group of incredibly-advanced psychic-cyborgs made in the Dark Age of Technoloy, designed to manipulate the Warp itself to allow for nearly instantaneous FTL travel. Malcador found The Emperor, serial name Oscar, and activated it.
So since Nobledark Emperor is specifically a man-made entity who's not that old in terms of life compared to the Real Emperor who's an immortal Warp god incarnated, he simply... Lacks knowledge of the Warp initially. He understands what it basically is and knows the threat of Chaos, but he lacks infomation on the deepr specifics.
Because of this, he actively seeks an alliance with the Eldar during the Great Crusade, because he's a reasonably minded non-xenophobic person unlike every human in 40K, since they are a millions old species with ancient archives filled with knowledge that no human could ever hope to obtain otherwise. The Eldar, who here have their arrogance downplayed but their sorrow and regret played up, are reluctant at first. Eldrad Ulthran comes to talk with the Emperor, and they discuss a way to form an alliance.
The two come to the conclusion that the best way to gain the favor of the Eldar would be to return the last survivor of their old pantheon to them, and so The Emperor + Eldrad + A fuckton of armies storm the Warp through the Eye of Terror, Empreror + Eldrad punch Nurgle in the face, (I told you the power levels are nerfed) and rescue Isha who incarnates in the material world. After this happens, Eldrad basically insists that the Emperor and Isha make a political marriage, because that would guarantee that the Human / Eldar alliance would last forever. And so they do, and have ruled the Imperium ever since.