This mission is only available if you chose to Redeem Eugene at the end of Heaven’s Hellfire .
It appears the Akurans have been rounding up the suspected "Bioterrorists" that were freed and plan to sell them back to the DUP. Head to the construction site and you’ll have to fight through a whole lot of Akurans, so make sure you retreat should you get low on health or your power. Once it’s clear, check the enclosed space on each floor of the construction site (destroy the boards with red Xs) to find the Conduits aren’t here.
After you check the third one, you hear choppers, so go to the roof and you’ll see them trying to get away with shipping containers. Luckily, Eugene will use his angels to keep the choppers close enough to where you can jump on the containers. Do just that and shoot the winch in the middle on top of the containers, then it will be lowered to the ground by Eugene.
There are a total of five containers and the last one will bring some DUPs into its vicinity. Take out the first wave and two large DUP agents, like the one you fought at the end of The Test will appear. Keep moving around and stalling until Eugene comes with a big angel, which prompts more DUPs to appear. When all DUPs are gone, the mission will be over.