JLA #11~Hostile Takeover
A short meeting and Lex Luthor dismisses his Injustice Gang with three days to accomplish their task.  At the Watchtower, Aquaman reports a section of ocean mysteriously disappeared during a sighting of his hologram counterpart.  Superman traced a laser broadcast to an orbital source and he and Martian Manhunter are preparing to investigate further.  (The energy field detected by Aztek and J'onn in #10 turned out to be the Genesis wave from the current DCU crossover.)  Batman calls in with news that someone has established an anti-JLA and are likely compiling a database of the League's skills.  A moment later a telepathic alarm comes in from Green Arrow who reports the missing piece of ocean just appeared in the San Fernando Valley.  Green Lantern leaves to help and he and Arrow clean things up.  Meanwhile, J'onn and Superman arrive at the broadcast point and find a skull-shaped satellite.  What they don't know is that it's actually a holographic decoy of the real satellite and is controlled by the Joker.  Joker turns the inside into a deadly maze, but J'onn is able to alter the shape of his brain to see it as Joker does, and guides them straight through.  Back in California, Green Arrow and Green Lantern are approached by a woman claiming to be a psychiatrist (actually Circe in disguise).  She uses smooth talking to try to turn them against the League.  Lantern begins to suspect something and leaves, but Arrow starts to take the bait and stays.  Batman makes a quick trip to New York City disguised as "Matches" Malone to speak with Plastic Man.  In the Watchtower, Metron of the New Gods makes a sudden visit asking for the League's help in finding an artifact called The Philosopher's Stone.  He says if he doesn't find it before Darkseid, there will be big trouble.  Aquaman dislikes the idea, but Flash sends a quick message to J'onn--which is actually returned by a telepath with the Injustice Gang--and receives the okay to go with Metron.  At the end of the holographic maze, the real J'onn finds a CD which Superman uses his optical scan to read.  Doing so, however, triggers a bomb that blows the entire satellite to pieces.  Back in Gotham, the only good news comes when Batman says the JLA has one advantage over Luthor--the corporate mind of Bruce Wayne.

JLA #12~Wonderworld
Green Lantern makes it back to the Watchtower just in time to see Metron alter the teleporters to create doorways into time and space.  He gives GL, Flash, and Aquaman each a "baby box" linked to his own Mother Box and sends them to find the Philosopher's Stone.  Lantern wasn't real sure of what was happening, but ended up in several unpleasant places where he thought he found the Stone, but didn't.  He ended up in a place called Wonderworld where he was luckily able to meet up with Flash and Aquaman again.  In the Injustice Gang's satellite, it's revealed that Luthor has his own alien running telepathic links, whom he has managed to keep sedated using his glowing rock.  When he sees the decoy satellite explode he can only assume Superman and Martian Manhunter are dead.  The two Leaguers use that opportunity to head back to Earth.  (Superman absorbed the explosion, except for the light it emitted, allowing them to survive.)  There, they pull a piece of rock out of a seabed about the same size as Luthor's satellite.  Supes sends it into orbit and he and J'onn rendezvous at the Batcave.  Meanwhile, Circe has convinced Green Arrow to help shut down the JLA.  He gives Luthor the computer access codes to the Watchtower.  Shortly after Metron leaves, Aztek gets a call from Luthor, learns he's shut down all outside communication, has been personally funding Aztek's training for this moment, and teleports 12 armed nuclear missiles into the Watchtower.  Luthor says if Aztek doesn't meet his demands, the Watchtower gets it and Aztek won't be able to warn others about some coming danger he knows of.  At the same time, Batman's playing his own game, hiring Mirror Master to spy for the JLA.  Back at Wonderworld, GL reveals that during his travels he ran into a futuristic AI named Hourman who informed him that Luthor has the Philosopher's Stone and Metron sent them on a wild goose chase to get them out of the way.  If they don't return to stop the JLA from beating the Injustice Gang, the Stone gets destroyed and Darkseid takes over Earth.  The guardians of Wonderworld refuse to get involve because they say they're waiting for the arrival of Mageddon, the Anti-Sun.  They do provide the Leaguers with a means of travel, though, and the trio uses their baby boxes to try to home in on Metron's signal.  They fly back through space and time thinking they've made it home safely.  It turns out Darkseid has overtaken Earth instead.

JLA #13~Wasteland
When Green Lantern, Aquaman, and Flash arrive on Earth, their bodies are in the form of pure light information.  They automatically enter the bodies of their current selves on Earth and find out it's 15 years after the destruction of the Philosopher's Stone.  The world has turned into a wasteland run by Darkseid's army.  They gather together what few superheroes are left to try to think up a plan.  Flash's body is in no shape for running, so he's unable to use speed to return them to their normal time.  Green Lantern has been brainwashed into Darkseid's swarmtrooper army, but comes to his senses and aids what's left of the JLA.  Aquaman decides if they can get ahold of some Apokolips technology they may still have a chance of preventing the Stone from being destroyed.  The Atom takes them to Las Vegas where Desaad made his base years ago.  They break into his lair and send Atom into the computer system, but are surprised when they're not met by opposition.  As it turns out, Batman tricked Desaad into downloading his mind into a software cube eight years ago and has been pretending to be Desaad ever since.  Seeing the other heroes motivates him to don his costume again and he tells them their first attack should be against the Moon.  In the meantime, Darkseid uses boom tube technology to bring himself to Earth where he is to begin transforming the world into a global concentration camp.

JLA #14~Twilight of the Gods
At Darkseid's zombie factory on the moon, two heroes, Azteka and Argent make their attack to shut down the mind control over all of Darkseid's troops.  Back on Earth, the rest of the heroes enter Darkseid's warship as the boom tube opens, expecting Desaad.  Metron is aboard and only his mobius chair can return Aquaman, Flash, and Green Lantern to the point in time they're supposed to be.  As the future's Wonder Woman distracts Darkseid and the Grandmother Box (formerly Granny Goodness), Batman tricks Metron into giving up godhood to experience what it's like to be human.  One punch takes Metron out and Aquaman, Flash, and Green Lantern leave with the mobius chair.  Wonder Woman and Batman are killed destroying the Grandmother Box, but not before they get to witness the moon's zombie factory explode.  Just then Green Arrow and the Atom burst in.  Arrow shoots a flare arrow, which deflects off Darkseid's personal shield, but because he can see, Atom turns himself into light and enters the villain's eye.  Inside Darkseid's head, Atom starts blowing things apart and Darkseid's mind explodes.  In the meantime, a now powerless Orion activates a Genesis Box which is programmed to convert the universe into pure energy and start over again---giving the JLA once last chance to save the Philosopher's Stone.

JLA #15~Stone of Destiny
(OK, this issue was double sized, so here we go.)  Using coordinates given to him by Mirror Master, Batman opens a teleporter from the Batcave to the Injustice Gang satellite.  In the satellite, Luthor gets a call from Ocean Master in the generator room saying he's just found the Joker bound and gagged.  That's when the Joker on deck with the others reveals himself to actually be Plastic Man.  Then the Gang notices the giant rock heading straight for them.  When Luthor orders it to be shot down, Green Arrow pulls his bow on him and reveals he's shut down weapon systems and the JLA is in control of the satellite's teleporters.  Superman, Batman, and Martian Manhunter enter and Dr. Light activates the Revenge Squad projectors again.  But Arrow takes the controls out, destroying the projections.  Dr. Light increases the light in the room to the frequency of radio waves, which blinds everyone and shoots Superman into space.  The room finally reduces to infrared levels again and the Injustice Gang activates special contacts which allow them to see.  Luthor starts using the Philosopher's Stone as a weapon, which allows him to do basically whatever he wants.  But J'onn releases the Gang's imprisoned alien who gets revenge on Luthor and Light (making things visible for everyone yet again).  Arrow and Plastic Man start dealing with the rest of them when Joker comes in with this huge gun and blows a whole in the alien's shoulder.  J'onn contacts Aztek in the Watchtower to tell him to get out, but Aztek's already disarmed the nuclear missiles.  Batman grabs the Philosopher's Stone which Supes (who bounced himself off a satellite near Jupiter and came back) is just about to destroy when a telepathic message comes in from Green Lantern to leave the thing alone.  Everyone teleports back to the Watchtower just as the giant rock collides with the satellite and blows both to pieces.  Metron meets them on the moon and it's explained that GL, Aquaman, and Flash were misled by an evil Metron from the possible future where Darkseid was in control.  Superman hands over the Stone, which Metron says is a phony, and Joker whips the real one out.  As he starts carving a giant grin into the face of the Earth, J'onn gets into his head long enough to make him sane and stop.  At that point, Luthor convinces him to undo all the damage in Star City, which, of course, clears Luthor's name.  Flash grabs the Stone and the Injustice Gang is free to go, because there was no longer proof they did anything wrong.  Metron takes the Stone but warns the League to be on their guard and prepare for "the fortification of Earth."  He leaves and delivers the Stone to Hourman in the future and tells him he must be Metron's successor.  Back at the Watchtower where things are semi-sane again, Aztek and Green Arrow both announce to Lantern, Flash, and J'onn that they're quitting the League.  But it doesn't much matter because Superman, Batman, and Aquaman emerge from conference minutes later announcing the JLA is officially disbanded.