Story
At the end of the Convergence event, Barry Allen, Supergirl, Parallax, Superman and Lois and their baby boy, Jonathan, travel to the past to prevent the Anti-Monitor from starting the Convergence. Their efforts are successful, and the multiverse is reborn. Superman and Lois choose to stay on the new primary Earth, arriving at the beginning of the New 52, and settle into a house in the country. Superman is apprehensive about this new world and how different it is from their own. They will have to adapt to this world together as a family.
Many years pass: Jon has grown, the family is living in California and has adopted new identities, taking the surname "White" (a tribute to Perry White). They keep a low profile and stay out of the lives of this world's superheroes. Superman continues his superhero duty quietly behind the scenes protecting the world without being seen and taking precautions to ensure no one discovers him and endangers his family. Lois has become an anonymous author, publishing several books under the alias "Author X", her books have helped uncover many criminal activities. Jon is unaware of his parents' secret activities and their real identities.
While Jon gets ready for school, Clark returns home after stopping a natural disaster. His powers have been in flux, but he can still get the job done. After Lois and Jon leave for school, Clark puts on his black Superman suit (an anniversary present from Lois many years early) and flies off to save the Excalibur Space Shuttle, piloted by Hank Henshaw, the future Cyborg Superman. If he can save the Shuttle, he can prevent Henshaw from becoming Cyborg Superman.[11] When a military team investigates the Excalibur crash site, they wonder why the Shuttle did not burn up on reentry, and a satellite photo reveals a humanoid shape steering the Excalibur shuttle. Meanwhile, in an alley in the city, Lois gives her contact, Cora, a flash drive containing her investigation on the criminal group Intergang. Lois and Jon's car is attacked by gunmen while driving home from school, Lois phones Clark about the attack. Clark easily defeats and disarm the men. After returning home, they conclude that Intergang was behind the attack, and must have followed Lois after her meeting with Cora.[12]
The next day, Superman arrives at the new Fortress of Solitude in the mountains, where he has taken Henshaw for medical attention after saving him from the Excalibur shuttle. Henshaw's vitals are erratic; Superman attempts to talk to Henshaw, who suddenly awakens and attacks him. Blanque, a psychic killer who Superman imprisoned in the Fortress many years early after he devastated an entire town with his psychic abilities, has taken control of Henshaw, and uses him to attack Superman, burying him under the walls. Blanque summons Henshaw to the Fortress' detention block to free him. Blanque says he had seen Superman's mind and knows there are two people close to his heart; a woman and a child, he intends to pay them a visit.[13] Elsewhere, Lois and Jon arrive in the city to make sure Lois' friend Cora is safe. Lois finds a note in Cora's office saying that Intergang has kidnapped her.
At the Fortress, Superman has recovered from Henshaw's assault and is searching for Blanque, who attacks him, throws him out of the mountain, and buries Superman beneath the mountain rocks.[14] Blanque and Henshaw make their way to the control panel, where Blanque receives a call from Lois. Blanque delivers a threatening message to Lois, but Superman punches Blanque into the wall. Blanque takes control of a Khund war suit and attacks Superman. Henshaw, who has regained control of himself, attacks Blanque with an energy blast. Superman takes the opportunity to throw Blanque back into his prison cell. Later, Superman drops Henshaw at the island where the Excalibur crash-landed and asks him not to detail their encounter. As Superman leaves, Henshaw pulls out the Oblivion Stone which he used to blast Blanque. When Superman returns home Lois shows him the note she found in Cora's office. Although Clark says Intergang needs Cora alive, Lois is nervous that she and Jon were approached by Bruno Manheim (the head of the Intergang) on the street in the city. Clark and Lois consider that maybe it is time to reveal to Jon that his father is Superman.[15]
Superman and Lois work together to find Cora. Lois calls Cora's phone while Superman uses his super hearing to identify the phone's location. Superman finds Cora in a cabin in San Francisco, and frees her, but Cora has already revealed Author X's identity to Intergang. Soon after, when Lois and her son Jon leave school, they are captured by the Intergang people. The men tie up Lois and Jon in the tool shed and set it on fire. This causes Jon's powers to emerge and, breaking free of his bonds, he opens the door through the flames. Lois realizes Jon has superpowers.[16] They are surrounded by Intergang's men, after escaping the shed. Superman arrives in time to disarm the men and flies Lois and Jon away. When they arrive home, Lois tells Clark that Jon has superpowers. Jon wants answers from his parents and is finally learning his parents' true origin. Clark and Lois explain to Jon that they come from an alternate universe, a universe different from this one. Their universe is gone, and this one is their home now, and the Superman and Lois he reads about in the newspapers are different people and part of this world. Jon asks why they lied to him; Clark explains they wanted to protect him and did not know if Jon would develop superpowers.[17]
Superman receives a vision of people being attacked by an alien Conqueror and flies to a government facility on an island where Hyathis is attacking Hank Henshaw and others. Hyathis wants Henshaw to give her the Oblivion Stone, but he only has half of the stone. She demands Superman to hand over the other half of the Oblivion Stone (found by Superman and stored in the Fortress of Solitude). Superman has no idea what the Oblivion Stone is, but remembers a necklace with a partial jewel found years ago. Superman and Hyathis are locked in deadly combat. Hyathis uses plants and vines to pin Superman to the ground, but Superman frees himself and pushes her back with a blast of heat vision. Superman gains the upper hand, and Hyathis is forced to withdraw. She promises to return to Earth for the stone.
Back at home, Jon cannot believe his father is a superhero and is reading about his adventures in the newspapers; saving people and preventing disasters. Inspired by his father's heroism, Jon attempts to fly, only to fall to the ground. Lois tells Jon to wait until his powers are properly developed. Clark is reunited with his family when he returns home. Lois tells Clark that the authorities have had an advance look at her book and are making widespread arrests; Intergang is finished. Jon cannot believe his life has changed so much in the past few days. Clark and Lois take him to the basement, where they keep a chest filled with things from their own world. One of the things is Superman's old costume. Clark gives Jon the Superman cape, and he attempts to fly with success. Jon has made his first flight and his parents watch with pride. Lois tells Jon "I always knew you were my little Superboy."[18]