Issue Superman 21
Subtitle You Can't go Home Again
Date September 1988
Writer(s) John Byrne
Artist(s) John Byrne, John Beatty
storyline Superman was flying back to Metropolis when he realized he was being followed. He doubled back and found a female dressed similarly to his own costume. She introduced herself as Supergirl, though she looked like Lana Lang. She told Superman that Lex Luthor had given her powers (including the ability to shape-shift). Superman believed that Lana had been brainwashed, too. He tried to help her, but she blasted him. When he got back to her, she rendered herself invisible and struck him again. Superman headed to Smallville where he found Lana and his parents tied up. They told him the dopplegangar had done it. He realized something and headed back into the sky.
He caught up to her and allowed her to chase him to Metropolis - she was confused and believed it had been destroyed. In her confused state, she called Superman "Clark." He took her to Luthor, but she didn't recognize him. He obviously knew nothing about her, either. He took her back out into the city and explained that she must be from another universe, and told her about recently meeting Superboy and the Legion of Superheroes. Her memory began to return - she'd seen him fight Superboy, but it happened ten years previous (in her time).
Supergirl took Superman to her reality and introduced him to her Lex Luthor.
Jimmy Olsen convinced Perry White to send him to Ireland in hopes of tracking the Silver Banshee. White agreed and told him Lois Lane would accompany him.

Issue The Adventures of Superman 444
Subtitle Parallel Lives meet at Infinity
Date September 1988
Writer(s) John Byrne, Jerry Ordway
Artist(s) Jerry Ordway, Dennis Janke
storyline Lana, Lex, and Pete Ross showed him their world was dying (and it was the same world where he'd met Superboy and the Legion). The Time Trapper had created their Earth and the Krypton from which their Superboy emerged. No other heroes or villains ever appeared on their Earth. The Time Trapper seemed to have lost interest in their world since the apparent death of Superboy.
Luthor had introduced himself to Lana and Pete at Jonathan Kent's funeral. He hoped he could somehow communicate with Superboy in the future - he believed he'd discovered a cure for Kryptonite poisoning. The trio visited the Kent farm. They found a secret room in the basement where Superboy kept some of his work. Inside, Luthor activated a device that showed him a man who claimed to be Superboy's uncle - he and two others were trapped in the "Survival Zone." Luthor, with their help, was able to free them and bring them to Earth. General Zod, Quex-Ul, and Zaora began bashing everything in sight - they were actually Kryptonian prisoners. In the ten years since they were freed, the three Kryptonians had taken over the planet. They'd also breached the planet's core, meaning certain doom to all live other than themselves. The only way they'd survived was the protective force field Luthor was projecting around Smallville.
Superman agreed to join the three, along with three other heroes: Bruce Wayne, Oliver Queen, and Hal Jordan, and go up against Zod.

Issue Superman 22
Subtitle The Price
Date October 1988
Writer(s) John Byrne
Artist(s) John Byrne
storyline Superman and Supergirl attacked Quex-Ul; Zod fried Bruce Wayne in his spacecraft. Hal Jordan and Oliver Queen were killed, too. Luthor got a message that their base was being attacked - Supergirl feared Pete was dead. Supergirl then appeared to be destroyed by Zod and Zaora.
Superman headed into the ruins of Smallville and found some gold Kryptonite. He hit Quex-Ul with it, permanently removing his powers. He fashioned a steel box and placed the powerless Kryptonian inside. He then did the same with Zod and Zaora.
Superman found Lex in his crashed ship. Luthor told him that Lana was one of the first killed - Supergirl was actually artificial life made from Lana's molecular matrix. Luthor died in Superman's arms. Superman and the three Kryptonians were the last living beings on that Earth. Superman hit them with green Kryptonite, which killed them.
Superman returned to his own Earth with the remains of the protoplasmic matrix of Supergirl. She was already beginning to reform. He gave her to his family and flew off to think about what he'd done.

Notes, references to time, and chronology:
  This story does not appear to have ever been reprinted.
Issue 21 references the incident where Superman was thrown through the time stream and met up with Superboy and the Legion of Superheroes (in Man of Steel vol 4)
  The protoplasmic matrix Supergirl makes her debut on this Earth.
  Superman executed three phantom zone criminals for murdering every being on an alternate Earth.

   
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