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AC (Aquaman) and new bride Mera blew up what appeared to be an oil rig, but was in fact secret holding facilities for the vigilantes who registered under the new Vigilante Registration Act.
Clark was ready to volunteer to be the first to submit to the VRA, but Oliver convinced him it would be better if he came forward, as his identity was already revealed.
General Slade Wilson captured Aquaman and escorted an initially willing Oliver to one of the holding facilities and tortured them for information about the whereabouts of the Blur.
Lois paid a visit to General Slade, who was overseeing the operations for the VRA, and took photos of blueprints of the facilities which ultimately helped Clark and Mera locate AC and Oliver. Lois was taken aback to find Tess working with Clark via satellite.
Mera found AC and Ollie and broke the latter out of a glass, water-filled cage and forced the water onto AC, to help him regain his strength and break from the chains.
Slade set off a self-destruct sequence, but then captured Clark in a Kryptonite cell, claiming himself ready to die for his cause. Just before the place exploded, Clark managed to use X-Ray vision to see the Omega symbol burned into Slade's brain.
Surviving the explosion, Clark came back to Smallville and had a chat with AC in the barn, who convinced him to bring Lois onto the team rather than leave her on the outside.
Lois had a discussion with Clark about how he shouldn't feel embarrassed or ashamed of his difficulty in facing the darkness, but should accept help from those around him. He agreed that he depends on her more than anyway, which is why he confided the secret about the darkness in her and no one else.
Lois convinced Clark to tell the rest of the team about the darkness, so he took her to the Watchtower for the first time and met with Tess and Oliver, telling them of the darkness taking over the planet.
In a final reveal, Slade survived the explosion and was being rehabilitated with some kind of metal patch over one eye, presumably to arise as the villain Deathstroke.