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Lois and Clark attended a screening of the Superman documentary in Metropolis. Superman had not been seen in over a year. After getting some pretzels, they headed home.
Lex Luthor was released - all 120+ charges had been dropped. While answering questions outside the courthouse, he was struck in the head by a rock. Others threw bricks, etc. at his waiting limo.
The next day at the Daily Planet office, Clark turned in an article on Intergang and worked on a Luthor story; Lois interviewed a man (K. Russell Abernathy) who was trying to develop Kryptonite as an energy source. After she left, something went wrong in the lab - Abernathy was hit with a laser beam reflected through the K and transformed. Green and spouting energy from his eyes, he nearly destroyed a city street before Clark could signal Supergirl. While she was taking care of the "Kryptonite Man," Kent was grabbed by some of Luthor's goons. He told Kent that due to his reporting, his reputation was destroyed. LexCorp was buying him out. He threatened Lois and broke a couple of Clark's ribs.

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Toyman burst into Luthor's lab in a Superman robot. Luthor, who was working with a Kryptonian memory crystal, told him to get rid of the "reminder" and pay a visit to Prankster.
Lois and Clark discussed Luthor and whether or not Superman's powers would ever return. Clark went in to investigate some unused subway tunnels, knowing they were linked to Luthor. He stumbled in on some men wearing the green armor that Luthor had worn before the Crisis. They saw him and attacked. Green Lantern (Hal Jordan) and Hawkgirl came to his rescue. After defeating the thugs, they dropped Kent off at his apartment. Hal gave him a GL ring.
Luthor met with Metallo.

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Clark told Hal he'd think about it and handed him the ring back. GL and Hawkgirl headed out on an emergency call - someone (or somethings) was attacking Stryker's Island Prison. Someone calling himself Uncle Oswald (the Prankster) took over the airwaves and created havoc by animating inanimate objects throughout the city. The "Flea Circus" broke the Kryptonite Man out of Strykers while GL and Hawkgirl took care of the Prankster's distraction.
The Krytponite man was taken to Luthor, who was also controlling Metallo. He extracted his Kryptonite heart and added it to his already HUGE collection of K.

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Clark and Jimmy teamed up to blow the whistle on a politician taking a bribe from Intergang. The police took care of the rest. He turned state's evidence against Intergang. Intergang then set it's sights on Kent.
After Luthor blasted K through Abernathy, two monsters (Neutron and Radion) attacked Clark, who was walking home. His signal watch to Supergirl wasn't working (like several other of his electronic devices lately), so he continued to flee on foot.
Luthor was using the Krytponite to pull something (which appeared to be a space ship) out of the Earth's core. He told Toyman that it had crashed into Texas years before Superman arrived, but had never been recovered.
Clark headed into a subway tunnel and was hit by a train. Satisfied that they'd done their job, Neutron and Radion left.

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Two days later, Clark (who'd survived the train) began getting some of his flight back. Lois found out and gave him his costume and her blessing.
With reports coming in that Superman had returned, Puzzler attacked the Daily Planet looking for Clark Kent. Superman appeared and took her down. Luthor got word that he was back. Intergang had an even larger ransom for Superman: Livewire, Silver Banshee, Bloodsport, Hellgrammite, and Riot were all on his trail. He quickly realized he couldn't take them all at once, so he began to even the odds. His flight returned in time to save Jimmy from being shot by the new Bloodsport.

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While hovering above his would-be assassins, Superman thought of the casualties of the Crisis and the loss of his powers. He knocked Bloodsport out, causing him to shoot Banshee and Livewire. Only Riot was left. After he was out, Kent returned to the Daily Planet office where he told his wife about his possible new powers - his brain seemed to be much more precise than it ever was. Perry White stepped out to give assignments on the Superman story, and Clark had to get out - he was getting overloaded. Superman flew into the sky above Metropolis hoping to get some control back. He focused and saw something below the city: Kryptonian crystals growing. Once they'd halted their growth, Superman went after Luthor.

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Luthor had rebuilt a Kryptonian battle cruiser and had his sights on an entire fleet. With the fight going full-on, other superheroes began arriving in Metropolis to help out.
Superman found the 'heart' of the ship and began focusing on it, but Luthor set loose blast after blast of Kryptonite. The ship then transformed into Kryptonite itself. Superman used all the power he had left to fly through it and grab Luthor. As they flew upward, Superman lost his powers again.
Together, Superman and Lex Luthor began to fall back to Earth.

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They landed on an island just off the coast. Both powerless, they fought on even ground. Luthor and Superman fell together. When Superman awakened, he was being loaded up by the Coast Guard, but he felt his powers returning once again. He flew away after learning Luthor had been captured and was en route to Stryker's.
Metropolis began rebuilding itself yet again. The Kryptonian ship reverted to its simplest form; Luthor's people said he was being mind-controlled by it.
Clark's parents sent him a manual typewriter due to his recent computer crashes. Superman later caught up with Jimmy and gave him back the signal watch. Jimmy gave him the Sunstone, which he'd found during all the madness. After taking down Dr. Virus and Kryptococcus and hearing that flying robots had busted Luthor free from Stryker's, Superman flew to the North Pole and planted the Sunstone. A new Fortress of Solitude was planted.