Post-Blast it was taken over by the Reapers and their Conduit leader, Sasha. It is used as their secret headquarters until it is discovered by DARPA operative Moya Jones. She sends her temporary partner at the time, Cole MacGrath, as the pair had been trying to stop the Reapers since Cole gained his powers. Inside, Cole fights through a veritable army of Reapers while besieged by Sasha's mind hallucinations.
As he comes closer to Sasha, he discovers how Sasha had been making the Reapers: Kidnapping the Neon District's civilians and loosing her mind control Black Tar hallucinogen into their systems. There is no Karmic Moment here, only freeing each of the prisoners before they turn into Reapers grants you five experience points.
When Cole arrives at the end of the Tunnel, Sasha has made a pit of her tar hallucinogen with a large pump which Cole must defeat her in. After he has defeated her, the First Sons detonate an explosive charge, runs in and kidnaps Sasha, while the tunnel is flooding over. This gives Cole no other choice than to flee into the Warren.
- It is possible to re-enter the Jefferson Tunnel after the collapse, if only through a glitch in the game. Simply repeatedly spam the jump button against the corner of the tunnel entrance wall, and Cole will appear on the other side. However, nobody remains and the most fun to be had is to mindlessly blow up the dozens of cars littered throughout.