In the present, Shadow Man makes his way to the Dark Engine after learning from Marco Cruz, a member of The Five, that his little brother Luke was located near there. He does see him, but is unable to reach him at first as the giant pistons were currenly active. Therefore, he is forced to travel to each Liveside location via the Cathedral of Pain to defeat the Five, later gaining access to the Soul Gates after activating them with a Prism which leads him to a different area of the Engine Block, depending on what gate he went through. From there, he would have to find each console to deactivate the pistons, though the first console was already available for access near the Dark Engine's entrance.
WIth all 4 pistons deactivated, Shadow Man is able to reach Luke, who turned out to be Legion instead, posing as his little brother to ensure he got there. Eventually the area was destroyed along with the rest of the Asylum upon Legion's defeat at the hands of Shadow Man.
END OF SPOILERS***