Writer: John Byrne, Jerry Ordway and Paul Levitz
Artist: John Byrne, and Jerry Ordway(The Supergirl Saga) and Various (the Conspiracy)
Publisher: DC Comics (1988)
Includes: Superman vol. 2,#21-22 and Adventures of Superman #444; and Legion of Super-Heroes vol. 3, #46-51
In the aftermath of The Time Trapper - Volume 1...
Clipped from Wikipedia:
...in then Superman: Following Superboy's disappearance from the pocket universe Earth, the Lex Luthor of that world is tricked into releasing Kryptonian criminals General Zod, Quex-Ul and Zaora from the Phantom Zone. They proceed to lay waste to the planet, eventually killing its entire population.
Having been summoned from the regular universe by Luthor and Supergirl, Superman executes the genocidal killers using green kryptonite, and brings Supergirl (a protoplasmic duplicate of Lana Lang) with him back to his own Earth
. ...in the Legion of Super-Heroes: While the entire Legion mourns Superboy's death, four members are particularly outraged: Saturn Girl (one of the three founders who invited Superboy to join), Brainiac 5 (who now realizes that all of his theories about time travel are incorrect), Mon-El (who regards Superboy as a brother), and Duo Damsel (who considers Superboy to be her first love, having once had an unrequited crush on him).
The four secretly enter into a conspiracy to attack and destroy the Time Trapper at the End of Time. With the assistance of Rond Vidar (who reveals himself to be the Green Lantern of Sector 2814), they barely succeed. However, another one of Duo Damsel's three bodies is killed, leaving her with only one.
Dork Note: This would be a great volume 2 to this death filled story arc.