Issue Superman / Batman 28
Subtitle The Enemies Among Us part 1
Date September 2006
Writer(s) Mark Verheiden
Artist(s) Ethan Van Sciver
storyline Bruce Wayne exited a charity event rather abruptly and headed down to the cave. After a short workout, Alfred brought J'onn J'onzz down. The Martian Manhunter attacked both Batman and Alfred. He told Batman that he had been abusing the term "hero" and continued his attack. Batman scared him off with fire.
The next day, he played back the recording for Superman. Superman noted MM hadn't had the aversion to fire in quite some time. As they went over the guest from the party (two appeared to be J'onzz), an alarm went off. A giant gorilla with Kryptonite-beam eyes was attacking Gotham City. "Titano" morphed and disappeared after a short battle with Superman. He became Parasite, then Dr. Phosphorus.
Superman hit him with a tidal wave of water. He and Batman were alone realizing this was just the beginning.

Issue Superman / Batman 29
Subtitle The Enemies Among Us part 2
Date October 2006
Writer(s) Mark Verheiden
Artist(s) Ethan Van Sciver
storyline The Martian Manhunter entered the cave, only to be blasted by a flame-thrower. Batman told him he had to make sure he was the real thing, then showed him the video. J'onn told him nothing (due to the "shoot first, ask questions later") and left.
John Stewart visited STAR Labs and began checking out his ring. He had a strange feeling about it. While testing, a huge green hand burst through the building and grabbed it.
Clark was almost duped by the shape-shifter in Lois's form. The real Lois attacked her and it turned into a Kryptonian cave man. Superman grabbed him and flew him into the sky. Green Lantern (Jordan) gave him a hand by encasing the creature in a ring construct. He took it to a containment facility out west. Superman then saw Batman, who told him Jordan had passed along word that he wanted to meet. Superman knew nothing about this meeting he'd supposedly called. Jordan then attacked them. Superman stopped him - his power ring had become corrupted and had taken control of him. Kilowog then attacked all three of them.

Issue Superman / Batman 30
Subtitle The Enemies Among Us part 3
Date November 2006
Writer(s) Mark Verheiden
Artist(s) Ethan Van Sciver, Marlo Alquiza
storyline Kilowog somehow got Superman on his side - the Kryptonian attacked Batman. He fought it off and flew the Green Lantern into the atmosphere.
Batman headed back to the cave. Alfred gave him a note from Commissioner Gordon. Lex Luthor wanted to meet with him. Batman complied. Luthor, who was teamed up with Plastic Man, showed him a planet sized celestial mass was heading toward Earth. Plastic Man and Batman headed to Superman's Fortress of Solitude. Starfire (or the shapeshifter posing as Starfire) attacked them when they got inside. Plas found what they were looking for - the blackrock - a Kryptonian artifact.
Superman and Kilowog fought on the moon.

Issue Superman / Batman 31
Subtitle The Enemies Among Us part 4
Date January 2007
Writer(s) Mark Verheiden
Artist(s) Matthew Clark, Andy Lanning
storyline Superman saw Kilowog's way and joined him.
Plastic Man, influenced by the blackrock, flew off. "Starfire" morphed into the shapeshifter's true form: Zook. A tiny orange creature. Martian Manhunter appeared. He, too, had heard the call which was going out to all aliens on Earth. Bruce left the two aliens and hopped back in the plane with Alfred. They headed out to catch up with Luthor.
Plastic Man got to him first. Luthor's men blasted him in hopes of getting the blackrock to remove itself from Plastic Man's body.
Ultra, the Multi-Alien, showed itself. Supergirl teamed up with them. Batman got to Luthor, but Supergirl, Ultra, and Superman all attacked him.

Issue Superman / Batman 32
Subtitle The Enemies Among Us part 5
Date February 2007
Writer(s) Mark Verheiden
Artist(s) Matthew Clark, Ron Randall, Andy Lanning, Don Hillsman
storyline Batman pulled Kryptonite on Superman. Batman took on the blackrock and returned to the aliens - to join them. Supergirl questioned her purpose in the situation and flew off.
Superman went to tell Lois good-bye, but she helped him break through. He then went out to save Batman. The controlled aliens gathered in Metropolis; Superman found Batman in the cave. They fought.
The alien invasion force arrived.

Issue Superman / Batman 33
Subtitle The Enemies Among Us conclusion
Date March 2007
Writer(s) Mark Verheiden
Artist(s) Joe Benitez, Victor Llamas
storyline With the aliens came more of the parasitic blackrock. Superman was able to get Batman out of it's hold - before he had to kill his friend.
Despero, who'd taken up with the alien "others," went to Luthor - he was the key. Without Superman, the Others would take over. Luthor would know how to kill Superman.
Superman went after the mind-controlled heroes; Batman set a nuclear bomb for 10 minutes. He was attacked by Jimmy Olsen, who had come into contact with the blackrock falling from the sky. Superman and Batman were taken before Despero and the Others. The Others saw into their minds and released the heroes. They'd only wanted to eradicate the Earth of humanity because Despero told them humans were evil. The Others saw the truth.
After a few days of healing, Bruce apologized to a woman he'd brushed off at the party. Superman and Batman later shook hands and solidified their once rocky friendship. B

Notes, references to time, and chronology:
Issue 29 depicts the Martian Manhunter in his new One Year Later blue outfit. He also mentions leaving the other guise behind.

   
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