While the shapeshifting Supergirl may have been spotted a few times in issues preceding this arc, we had no idea of her identity or why she had been found in Antarctica. 

Superman (1987) #21 opens on the domed city she calls home- surrounded by land that looks almost like the moon, it’s so desolate. Inside the complex, Lex and Pete discuss how dire their situation is- all of their hopes for survival rest on Supergirl and Superman coming back. We can see more survivors in matching armor in the complex behind them, going about their work. 

Then, Clark realises he’s being followed, and he doubles back to reveal.. Supergirl! When he seems shocked, she shapeshifts in front of him, revealing herself to be Lana Lang. Much to Clark’s confusion, she says Lex Luthor gave her these powers- when he knows Lana hates Luthor.

As they talk, Supergirl gets more and more confused and distressed, eventually blasting Clark away because she thinks he’s trying to trick her. Clark makes his way to Lana’s farm, where he finds.. the Kents and Lana tied up and gagged? Lana warns him that there’s some crazy superwoman out there who looks like her- and Clark says that down to the molecular level, Supergirl is Lana. He’s checked. 

Clark has an idea as to how to get Supergirl to come to her senses- he leads her to the Lex he knows, old and bald and yelling into his phone in a business suit. Supergirl seems confused for a moment before remembering- and taking Superman to her universe.

Adventures of Superman #444 opens on Clark in front of his parents’ graves in the pocket universe. Lex and Pete and Supergirl stand behind him.

Then, Lex explains the existence of their world. The Time Trapper apparently reached one million years back into the past to remove a sliver of time. He then pruned that sliver of time, erasing billions of lives, until all that was left was Krypton and Earth. The rest of the universe was completely empty- no stars, no planets. Then, he prevented every hero and villain origin story except Superboy (Clark Kent)’s. 

After the death of Superboy, Lex Luthor was tricked into releasing three Kryptonian criminals from the Phantom Zone. As thanks, they spare his life- and then become genocidal dictators over Earth. They decide that the only way to stop the human resistance they are facing is to simply eliminate all life on Earth. They bore through the Earth from three different directions, trying to make the planet uninhabitable. They would have succeeded completely, if it weren’t for Lex’s force field dome protecting Smallville.

Lex claims he found a way to give Lana Kryptonian-like powers, but she alone was not strong enough against three full-blooded Kryptonians. So he sent her across universes and time to try to recruit Superman to their cause. 

Superman (1987) #22 opens on the void of space behind Clark as he stands on the desolate land of this Earth. We find out that by now, all life on Earth beyond Clark and four others has been destroyed. We watch the crew we met before- this universe’s Bruce and Oliver and Hal- get picked off by the Kryptonian criminals. Supergirl, horrified and upset, rushes into the fight against them and gets blasted by two of them at once.

She seems to catch on fire and melt, turning into this purple goo humanoid and falling down onto the surface. There’s no time to help her.

Lex and Clark are the last conscious beings standing in defense of Earth in this entire universe. Lex gives Clark instructions to his final plan, telling him where he can find gold Kryptonite (removes a Kryptonian’s powers) and green Kryptonite. Superman rushes through the plan while Lex stands alone against them- when Clark gets back with the pieces in place, Lex is already dying.

On his deathbed he reveals that he had the Kryptonite all along and had a way to stop this suffering from the beginning, when he first stumbled upon Superboy’s lab. But his pride refused to allow him to fix his mistakes with even a dead Superboy’s technology, and so instead he tried to create an artificial being to replace him.

He reveals that Supergirl is not Lana Lang, and that he implanted Lana’s memories within her. The real Lana Lang died almost immediately after the genocide began. Supergirl is instead a protoplasmic being, completely unaware of her own artificial nature. 

After Lex dies in his arms, Superman puts his plan into place, finding the trapped Kryptonians. After some talking with them, he realises he has no option but to kill them- he can’t allow them to follow him to his home universe and he has no way to trap them. 

He finds Supergirl afterwards, collapsed somewhere in the desolate landscape. He brings her home to his parents- the ones she kidnapped- and asks them to take care of her for him.