Krypton is on the verge of civil war, with the uprising of a rebel movement called the Sword of Rao. At its head is General Zod, who used to be a close comrade of Jor-el, the leading scientist of Krypton. Their friendship reached breaking point when Zod chose to trust Krypton's pre-emminent AI, Brainiac, over Jor-el's judgement with regards to the planet's impending doom. This doom was wrought by the extensive mining of Krypton's natural resources, which resulted in the core of the planet becoming unstable. Zod had been blinded by his desire to increase the militarization of his army to combat the hostile forces of Apokolips, at the expense of the planet's well-being, while Jor-el managed to convince the high council to act against his forces. A small coalition of the military broke off and joined Zod's revolution, while the rest swore their allegiance to the council and Jor-el.
The conflict had distracted the Council from implementing measures to save Krypton's core, which was now Jor-el's sole responsibility. he worked hard to disable Brainiac's influence on the planet, but unbeknownst to him the AI had developed exponentially throughout the years as a result of the complacency of the Kryptonians. With no one to keep a check on him, Brainiac soon became self aware and decided to rid the galaxy of what it perceived to be a blemish.
Jor-el realized that the time-frame for him to stabilize the core was too short, and made an impassioned plea to the council to evacuate the residents into an inter-dimensional portal called the Phantom Zone, while he stayed behind on Krypton to make sure the stabilization was successful. His plea was interrupted when Zod intervened, having finally defeated the council's forces. He ruthlessly killed the leaders of the planet, before making a final attempt to recruit Jor-el to his new regime. Jor-el could not recognize his old friend from the monster he had become, and reacted quickly to imprison his friend in the phantom zone, telling him that doing so will save his life. Zod however was consumed with hatred and rage, as everything he had fought for was now snatched away from him by his oldest friend. He viewed the act as a betrayal, and warned him that he will bring the House of El down and exterminate every single member with his own hands.
Meanwhile back at the House of El, Lara Lor Van was preparing for the ignition of their spacecraft, which will take them to a far away galaxy with a yellow sun. She waits for Jor-el's arrival but Brainiac shows up instead, in meta-human form. He destroys the spacecraft and captures Lara as leverage against the only Kryptonian standing in his way, while unknowingly leaving behind her new born child in the rubble.
Jor-el meanwhile enters the Kryptonian Circle, a platform which allows for mass communication all over the planet. He installs several portals in accessible areas in capitals all over the planet, and informs the residents to evacuate immediately. However his broadcast is cut short by Brainiac, who arrives at the chamber. He orders Jor-el to disable the portals or he will kill his beloved wife in front of his eyes. Jor-el struggles with himself, but decides to act on the greater good and heroically jams the controls, leaving them unusable and impenetrable to Brainiac, who would be unable to override the command. In a fit of rage, Brainiac twists the neck of Lara, who dies instantly on hitting the ground. Jor-el dashes towards his wife and grieves over her lifeless body, while Brainiac invades the system in his AI form, determined to reverse Jor-el's commands. That proved to be unnecessary however, as the exploding core had finally overcome Jor-el's protection and was now on the verge of disintegrating, in the process destroying all of the portals.
To ensure the safety of his son, Jor-el had no choice but to leave Lara behind at the chamber. He goes back to his house only to find the spacecraft in ruins. He collapses on the floor in grief, only to hear the crying of his son beneath the rubble. He excavates him from the ruins of the ship, and is surprised by how little damage baby Kal-el had sustained from the explosion. Jor-el initiates the emergency spacecraft which only had room for one. Placing Kal-el into the pod, Jor-el tells him of his great destiny, to one day rekindle the hopes of the Kryptonian people, as the last of his kind. He places a metallic crystal in the shape of his family emblem, on Kal's chest, before activating the ignition of the pod. Kal-el blasts off into the red sky, amidst the beams of lava blowing up from the ground.
As Kal's pod begins to activate a space warp, krypton explodes in a shower of debris and light, as fragments of the planet shoots out into the unknown reaches of space. The pod soon disappears into a swirling tunnel of space and time, and on towards the planet Earth.
As the remains of Krypton floats around space, another space warp appears in its proximity. A huge skull like ship with four pincers attached to it, zooms out of the wormhole. A large glowing net of lights envelop the dark matter surrounding Krypton's remains, which had been imbedded with Brainiac's consciousness. When the process was done, the skull ship disappears back into the wormhole, on towards a fiery planet known as Apokolips.