After Batman and Batwoman left, Clark and Hal stayed behind in Batwoman's universe to handle the aftermath. So-called cleanup mostly meant watching Atlantis and making sure they did not fight hard enough to affect the land.
Atlan harbored nothing but hatred for present-day Atlantis, and the Atlanteans clearly did not recognize this New King at all. Their conflict erupted far more violently than expected, and in the end, Clark and Hal had no choice but to move the Sea Queen onto land.
They found a note Batman had left for them in Batwoman's Batcave. It explained in detail what Batwoman had encountered, as well as the contamination that mysterious meteoric metal might cause.
Realizing something was wrong, the Sea Queen could no longer afford to dwell on old grudges. With Clark and Hal's help, they sealed Atlan back beneath the sea and began inspecting Atlantis's energy system. Sure enough, they found a problem with the filter at the outlet.
There was ample evidence that the contamination had not come from the continent at all, but from Atlantis itself. And the contamination within Atlantis had most likely come from some mysterious piece of metal.
After conducting a thorough search, the Sea Queen finally found the culprit. It appeared to be the central core of a filter. After Hal wrapped it in Green Lantern energy and scanned it, the contamination reading immediately dropped.
In the end, the Sea Queen chose to hand the thing over to Clark and Hal before returning to Atlantis to restore order there.
Clark and Hal held this hot potato and had no idea where to take it. Just then, Bruce called Clark and invited him on a long trip, so Hal decided to take the thing and visit this universe's little Blue Men.
Never mind whether the