Right, so here's my idea for a Superman sequel, since at this point they've already restarted the franchise as much as they're going to (for which I'm very happy to have the Superman universe no longer include Richard Pryor or a solar-powered Nuclear Man).
We pick up a couple of days after Superman Returns. Superman, in a lead spacesuit (he said, borrowing from the animated series) retrieves the Kryptonian crystals from the asteroid and gives it a kick for good measure, sending it fast on its way out of the solay system.
SUPERMAN: Maybe now the tides will get back to normal.
He looks back down at Earth and uses his telescopic vision to see that the beginnings of a tsunami have already started. He flies down to deal with it, but we don't go with him. Instead, we soar through the stars as the credits roll in Superman-style, until finally we reach the Skullship, deep in the void of space. Yes, THAT Skullship.
Brainiac laments the lack of a breakthrough in his experiments to his repairman/beta tester and organic sidekick (because even evil sentient computers need someone to bounce exposition off), Koko, a monkey-like alien. And yes, I know Koko is a wacky Silver Age plot device, but I trust everyone involved can make him, if not cool, then at least not embarrassing. Koko is a prisoner of Brainiac who's forced to check for errors and repair damage Brainiac cannot himself correct. He's basically there so that Brainiac can try to understand the "human" condition. As Brainiac explains it, he's a control sample. Brainiac constantly and cruelly makes him think he's about to die, just to see his reaction.
Once, long ago, someone asked Brainiac if there's life after death. Brainiac, being the literal sort, observed people on their deathbed to gauge their reactions to death. Then he started killing people. Then he started destroying entire worlds to see how civilizations as a whole would react to destruction. Everywhere he goes, the reaction is the same. Attempts at appeasement, denial, fear, panic, insanity, etc.
Then he (it?) picks up the gravity of the Kryptonian continent passing through space. He tracks it back to Earth, where his sensors pick up an excess of neutrinos (particles related to time, Brainiac says that the local time-space continuum has been pushed nearly to the breaking point, like a black hole, explaining why Superman doesn't reverse time because the effect is cumulative).
BRAINIAC: Earth has nowhere near the resources necessary to develop interplanetary projectile weaponry. They're only a sixth-level intelligence.
KOKO: Then you're twice as smart as one of them?
BRAINIAC: No. All of them PUT TOGETHER are a sixth-level intelligence.
Then his sensors pick up traces of Kryptonian "exhaust gas."
BRAINIAC: It could only mean one thing.
KOKO: You mean...
BRAINIAC: The son of Jor-El yet lives. A Kryptonian raised by... "humans." I wonder how he will react to his deletion.
They set course for Earth, where they find traces of Kryptonian radiation. Naturally, it's coming from the guy who's been exposed to Kryponite the longest... Lex Luthor. Brainiac cloaks his ship and lands on that desert island where Lex and Kitty are still trapped. He tests humans' reaction to death by killing Kitty in cold blood.
KITTY: Lex, do something!
LEX: Why?
Then Brainiac begins to interrogate Lex as to Kryptonian technology.
KOKO: This is pointless. Just kill him and be done with it. We're not getting any closer to Kal-El.
Needless to say, this sets Luthor off and he quickly wheels and deals his way into Brainiac's good graces by promising him Kal-El. Lex explains that if Brainiac can't detect Kal-El right now, it's probably because he's in the Fortress of Solitude and shielded from his probes.
BRAINIAC: Earth custom would dictate an expression of gratitude at this point. "Thank you." Your modification from biological unit to biological waste will be as smooth as possible and added to my databanks for future edification.
LEX: Wait, wait! Just give me five minutes.
BRAINIAC: Minutes?
LEX: (immediately) 1/535680 of the time it takes for this planet to rotate around the sun... roughly.
He explains that the light of the yellow sun gives Superman god-like powers and, moreover, that he has the support of all the world's nations behind him. "The UN made him a citizen of every country on the globe." But, Lex says with a glimmer in his eye, "you scratch my back and I'll scratch yours."
Brainiac extends claws from his hand before Lex waves him off. Separate Superman from his adoring public, Lex explains, and he's powerless. He needs the mindless adulation of the unwashed masses or he's just a guy in silly tights. It took five years for this to happen naturally, but Lex can do it in two. Brainiac says this is inefficent.
LEX: On the contrary, it's scientific. I've met him, guy has a martyr complex the side of this island. You kill him, blip, it's over, just like that. Not very satisfying, trust me, I've thought about it. But you break him first... then we'll see what really beats in that alien heart he's draped a red cape of humanity over.
Brainiac accepts.
Cut to a few years later (whenever the film is released to you and me). Lex has invested what remains of his fortune and, with Brainiac's help (alien technology patents, manipulating the stock market with a twelfth-level intellect), has made himself a billionaire. Still obsessed with land, he's made himself a mover and shaker in Metropolis and basically owns the entire city. He's also pulled a Rupert Murdock and made his own news organization to compete with the Daily Planet, Lex News, as well as formed a special interest group, Citizens Concerned About Alien Influence (CRAAL, pronounced "crawl"), to basically muck-rake Superman.
On a morning talk show on Lex News, Lex argues with guest Lois Lane about Superman.
LEX: You see a savior, I see an unreliable alien that's keeping us from reaching our full potential. I see us becoming more and more dependant on him to solve our problems, human problems... and I can't help but wonder what happens if and when he cuts out for another five years? Or longer? Or forever?
Lex goes on to imply that Superman framed him for the nuclear weapons plot and asks what if Superman is just the vanguard for an alien invasion, name-dropping that there have been sightings of "strange beings" in St. Roch, Coast City, Central City, etc. Maybe with a few blurry "Bigfoot" style pictures of superheroes just for fun.
Cut to Clark Kent watching this at the Daily Planet, where he looks guilty. A lot of the public has lost faith in him and a Lex News poll shows his approval ratings down. "Up next," Cat Grant, the Lex News anchor, announces. "A special on the damage Superman could do if he went rogue using the very latest in special effects technology."
However, this is a Superman movie, not a "Clark Kent has angst" movie, so we zoom in on Kent's ear as he hears "Help, Superman!" He checks with his x-ray vision... people in the elevator, two interns necking in the supply room... and finally takes the stairs at superspeed, the gray blur of his suit transitioning smoothly into red, blue, and yellow.
In a museum, a gang of high-tech banditos (maybe led by a minor Superman villain doing a cameo), steal several gems... and a sample of Kryptonite inside a translucent lead display. They smash the sample with a sledgehammer, takes a finger-sized chunk, saying "This is all we need."
Superman flies through the city. "Look, it's a bird!" and so on.
On the roof of the museum, the gang loads their loot into a helicopter gunship. One technician installs the Kryponite fragment into a strange-looking cannon installed on the nose.
Then they hear the sonic boom of Superman approaching.
TECHNICIAN: It's not ready yet!
LEADER-CAMEO-VILLAIN-GUY: Then we'll have to buy some time, won't we?
He detonates some explosives in the foundations of a monument (ala "the Washington") on the other side of the city. Superman's eyes glow red with anger, but he abandons the thieves to save the collapsing monument. He catches it before it falls into traffic, pushes it back into place, then freezes the foundation with his Arctic Breath. This done, he grabs a cement truck and squeezes it like a tube of glue, replacing the ice with cement which he then drys with heatvision. Bam, the tower is as good as new. Superman polishes a smidge off it with his cape and goes after the thieves, who are getting away in the gunship.
What follows is a spectacular dogfight between Superman and the helicopter through the urban canyons of Metropolis. The helicopter has a Kryponite laser which weakens Superman for the missiles and miniguns of the helicopter. Superman uses his X-ray vision, looking for something made of lead. He finds the sewers. Lex Luthor got a contract to renovate them and made them out of lead to spite Superman. Supes rips up a sheet of metal and uses it as a shield to get close enough to grab it by the tail and spin it around, trying to nauseate the thieves into surrender. The leader opens up the laser and takes out the Kryponite, throwing it at Superman.
It hits and Superman is weakened, letting go of the helicopter. It crashes into a skyscraper under construction. Superman rescues some workers and the thieves, but the skyscraper is pretty banged up.
A limo arrives. Lex's new, not-annoying hot babe sidekick, MERCY GRAVES, opens up a lead ringbox and hands him a Kryponite ring (Lex: Amazing the things you can find on E-bay). She's a fanatic who came up through the ranks of CRAAL and, as Lex explains, "she has a conscience I can buy."
Lex goes to confront Superman, taunting him to keep his distance and demanding to be reimbursed for the damage to "the new Lexcorp Tower" or he'll sue.
SUPERMAN: Sorry, left my wallet in my other tights. But if you'll give me a minute...
In a pure Silver Age moment, he flies deep below the sea, to a sunken ship wreck, grabs a treasure chest, and drops it in front of Lex. Lex's eyes go wide as Kal-El hands him a ruby.
SUPERMAN: That should cover the damages. I'm sure you'll see that the rest goes back to the proper owners. It was a Spanish galleon, seventeenth century I believe, but I didn't get a good look.
He flies off, leaving Lex to simmer. Or tries to. He has to embarrassingly walk a few more meters away from the Kryptonite before he can "up, up, and away."
More to come.