The Parent Swap

Superman and Supergirl are nearly defeated by Atlas and Brainiac in different stories in the same month.  We get a glimpses of several parents who were believed dead and who will play a big part in the coming year.  As other characters' parents return, one of Superman's won't live to see the end of the current story.

Superman #679

The Coming of Atlas part 3 of 4

Superman struggles against Atlas, but finds that he may be outmatched in this fight.  At LexCorp, CEO Lana Lang desperately looks for a way to help Superman, but in doing so she inadvertently activates a hologram of Lex Luthor who promptly fires her for violating a clause of her contract.  While Jimmy Olsent photographs Superman and Atlas, he sees a mysterious figure on top of a building watching the fight who he thinks looks familiar.  Supergirl hears the fight and rushes to Metropolis to help her cousin, but she's shot down by a blast from a satellite in space, marked as "Hotel 7734."  With Superman and his allies all fallen, Superman's loyal pet Krypto arrives on the scene to defend his master.

Action Comics #869

Brainiac part 4 of 5

Supergirl bravely takes a stand while Brainiac's ship attacks Metropolis, aided only by the staff of the Daily Planet.  Aboard the ship, Superman finds the Bottle City of Kandor, and also discovers that Kara's parents, Zor-El and Allura, are both still alive.  They had survived the Krypton's destruction on Argo City, but Brainiac later found them in space and trapped them inside the Bottle City with the other surviving Kryptonians.  Brainiac covers Metropolis in a force field and fires a missile into the sun, which will destroy it and Earth the same way that Krypton was destroyed.  From Smallville, Ma and Pa Kent see the shot fired into the sun.

Superman/Batman #52

Lil' Leaguers part 2 of 2

The lil' villains attack Metropolis and Batman is stuck at the Hall of Justice on monitor duty watching the Lil' League while Superman and the rest of the Justice League go to the scene of the action.  Lil' Lex Luthor leads the villains into the Hall of Justice to the JLA trophy room to find the Father Box, which he calculates is bigger and more powerful than the one in their universe.  The Lil' League learns the hard way that this world is more dangerous than their own when their Superman is killed stopping Lil' Doomsday.  Mr. Mxyzptlk and Bat-Mite were just trying to have some fun with this multiversal crossover, but unfortunately their 5th dimensional powers can't raise the dead.  Their innocence lost, the Lil' League is sent back to their dimension along with the villains, except for the Lil' Joker who stays behind to find his counterpart at Arkham Asylum.