This was an idea I had for a sequel to Man of Steel... It isn't very good.
One year after the Battle of Metropolis, Lois Lane is constantly followed by federal agents, who believe she knows how to contact Superman, making it difficult for her to be seen with him. She has however begun a relationship with new journalist Clarke Kent. Superman sightings have become non-existent in Metropolis but there are consistent reports of him helping in other cities. Despite him initially helping in the rebuild efforts, there is a rising Anti-Superman sentiment. Lex Luthor is elected president on a campaign where he vows to protect America from future alien invasion. He claims to be able to control Superman but refuses to reveal how.
At the Daily Planet Lois Lane is investigating LexCorp's investments, including a mining operation in Arctic Canada. The operation is close to the site where a kryptonian ship had been hidden twelve months earlier and involves a huge dug out crater at the bottom of a mountain. She is captured when she discovers they are mining the remains of the crashed Kryptonian scout ship. She notices a large Hercules class plane that is co-branded with Wayne Enterprises Logistics and LexCorp Transport. Superman arrives to free her and easily defeats the Army guards. However, the cargo hold of the plane opens to reveal three robots that attack both. After easily defeating two of the machines, Superman is weakened by the third, which has glowing green gauntlets. LexCorp employees, guarded by military personnel, film the encounter. Lois eventually swings a crane into the arm of the machine, damaging the gauntlet. Superman is able to remove its head and in anger throws it towards the north pole. He attempts to use his heat vision to destroy the Hercules but is unable to muster the required energy. Feeling depleted he scoops up Lois and flies back to American soil.
Upon return to Metropolis, Clarke Kent becomes unwell. Desperate to know more, Lois travels to Gotham City to interview Wayne Enterprises President Lucius Fox. Fox reveals that WE is helping to fund the LexCorp operation as part of a government defense contract but refuses to reveal more, citing the top secret nature of their military contract. When she is escorted out, she is complimented by a younger Wayne employee who says he can tell her more. Eventually he reveals himself to be Bruce Wayne, eccentric billionaire. He shows Lois the camera footage from the Arctic battle and notes that the substance used is alien and can weaken Superman. He offers to help but Lois does not reveal Clarke's secret.
In Metropolis Luther publically releases the footage of Superman fighting the army up north. The footage does not reveal the robots or show Superman weakened. Supported by psychiatrist Professor Milton Fine, he declares Superman an enemy of the state and orders his arrest. Lois is arrested for aiding and abetting a fugitive and transported to a secure facility. Wayne contacts Clarke and meets with him. He reveals that Luthor has obtained an alien crystal from the ruins of the arctic ship. He also admits he knows Clarke is Superman and tells him, "you don't think the glasses are fooling anyone do you?" Clarke neither confirms not denies. Wayne reveals Lois is likely imprisoned in the Navada desert.
Luthor interrogates Lois himself. Lois asks Luthor about the substance, which he calls Kryptonite, and confirms he wants Superman to give himself up and join the military. Lois continues to resist Luthor so he calls for 'him.' Telling Lois that Superman has changed things - he has changed what is possible. Luthor calls for Professor Fine to enter. A hooded man enters the room and does not speak. Fine removes his hood, revealing diodes running out of his head. He touches his hand to Lois' head and merges with her brain. Her memories are transferred to the alien and she collapses unconscious. He nods to Luthor and communicates telepathically with him - he knows that Superman will be on his way.
Superman arrives but cannot break through the facility's walls because they have been laced with Kryptonite. Stuck outside he is surrounded by helicopters, tanks and armoured vehicles. Weakened, he is beaten by military strongmen in Kryptonite enhanced armour. Unwilling to risk killing them Superman does not resist and is taken into custody. The footage is played across the world as Luthor declares the War on Superman over.
Superman is placed in a cell with Lois. She does not recognise him, despite him trying to jog her memory. Luthor faces Superman himself. He offers him the chance to join the military. Clarke refuses, declaring his loyalty is to the people of earth - not a military ruler. Professor Fine emerges from the darkness and calls him Kal El. He introduces himself as the Brainiac - a being of Krypton who was part of the artificial intelligence in the original scout ship. He tells Clarke he is programmed to ensure the safety of Krypton and that he needs Clarke's help to do so. Luthor begins to get nervous and asks what is happening. Clarke tells him that Braniac means to kill him. Luthor orders the Braniac arrested but the military are unable to restrain him. Brainiac escapes into the desert and heads for Metropolis. Clarke is unable to stand due to the restraints and asks to be freed so he can stop brainiac. Luthor reluctantly agrees and Clarke leaves with Lois.
He is unable to fly so they begin walking until a Wayne Enterprises jet meets them. The pilot informs them that Mr Fox asked that they be escorted to where ever they want to go. Fox has also supplied a Wayne Tech suit that absorbs the sun's radiation and heats the body. It is black and already has the House of El shield emblazoned on it.
In Metropolis, Brainiac uses LexCorp construction vehicles to rebuild parts of the city to resemble Krypton. Using his enhanced powers he is able to rebuild skyscrapers as defense towers.
Clarke returns to Metroplois and, with help from Perry White, arranges a national broadcast. He apologises for the destruction of the city a year before and plays a video of Luthor conspiring with Braniac, supplied by Wayne. He calls on Braniac to meet him in the arctic to settle the score.
Clarke and Braniac battle at the North Pole. The battle rages across the arctic, south towards Canada. Frustrated, Braniac uses projections of his Jor El to convince Clarke to surrender. Clarke eventually resists and weakens Brainiac using a kryptonite laser supplied by Wayne. He uses his ice breath to freeze Braniac. Rather than kill Brainiac, Clarke imprisons him in the remains of the LexCorp crater in Canada, and causes the mountain to avalanche into the crater. Brainiac, and the last remains of the Kryptonite, are buried within. Superman rips the black suit from his body, revealling his usual blue costume beneath. Still weakened by his exposure to the Kryptonite Superman submits to the Canadian military, acknowledging that in order to help others he needs to play by their rules.
Clarke Kent returns to work for the daily planet, on the day Luthor is impeached, and is called into Perry White's office. He sends him on assignment to Central City where rumours are circulating that another 'superhero', dubbed The Flash, has been fighting crime. Before leaving he visit Lois in hospital and promises to do whatever he can to restore her memory.
Sometime later, beneath the collapsed mountain, the remains of Brainiac melt and are fused with the corpse of a nearby kryptonian solider. The corpse begins to mutate. It's eyes glow red as the creature is reanimated amongst the rubble. Doomsday is born.