After the two have an argument during a drive, which mostly concerns Clark frustration over his true ancestry and how he is forbidden to reveal his powers to anyone but his parents, they stop when a tornado forms, threatening everyone on the road nearby. Clark gets his mother and several others to safety, with Jonathan attempting to get the family dog free of their vehicle.
The dog makes it out safety, but Jonathan ends up injuring himself, unable to make it to the overpass where everyone has taken shelter. Clark had wanted to help his father, but a gesture from Jonathan cautioned him to not reveal himself, leaving Jonathan to be swept away by the tornado. Hearing his story, Lois respects Clark's wish for privacy, and stops trying to pursue a story from him.
Clark returns to his mother, and happily tells her that he has found where he came from, and who his true parents are. Though Martha fears that her son will now be taken from her, Clark assures her it won't happen. Meanwhile, the military has received word of a strange ship in geosynchronous orbit around the planet.
Soon, others report the strange sighting, but are surprised when power is cut off to all parts of the world, and a message is broadcast from General Zod. Zod demands that the people of Earth hand over Kal-El within 24 hours or there will be consequences. A worldwide manhunt is initiated to find this Kal-El.
Glenn Woodburn is interviewed about the aliens and drops Lois' name, which soon results in numerous FBI agents being sent to take her into custody. Lois tries to flee from them, but she's quickly intercepted and turned over to the US Army.
Back in Smallville, Clark goes to a local church, and confesses to the pastor there that he is the one the aliens want. Though he admits he is conflicted: he doesn't trust that Zod will leave Earth in peace, but he is also wondering if he should trust humanity. His decision is made when the Pastor tells him that sometimes one must take a leap of faith.
Clark then appears before the Army in his Kryptonian suit, willing to surrender on condition that he can meet with Lois and that she be freed. Clark is handcuffed (he allows them to, as a gesture of trust and to help them feel more secure), and he and Lois have a short conversation. She asks him about the "S" on his chest which he tells her is not an S as Earthlings know it, but a symbol of hope.
When she suggests a new moniker, her voice is cut off by feedback from the audio system observers are using behind a 2-way mirror -- but Clark shows he is easily able see through it and identify the people standing behind it. Clark stands up and effortlessly breaks his handcuffs and tells the observers he'll allow them to turn him over to Zod and that he'll protect the planet from whatever danger Zod presents.
In a remote desert, a black craft appears to bring him to Zod's ship. The craft is commanded by Faora-Ul (Antje Traue), who also demands of General Swanwick (Harry Lennix), that Lois also be taken with them. Though Swanwick points out that the deal was originally for only Kal-El to be handed over, Lois goes along.
Before they reach Zod's ship, Lois is fitted with a breathing apparatus, as the atmosphere on the ship will be toxic to humans. When Faora is distracted, Clark slips Lois the key he used to restart the Arctic ship. On board the ship Zod welcomes Clark, who few moments later collapses to the floor of the ship, seemingly unable to breathe.
Though Lois is worried for him, Zod assures her that Clark's body is simply adjusting to the Kryptonian atmosphere aboard the ship. Clark passes out, and finds himself in a dreamlike vision of his family's farm. Zod explains to Clark that after the destruction of Krypton, the portal to the Phantom Zone where they were trapped was opened again.
After modifying the portal's Phantom Drive, they were able to transport themselves all across the galaxy in the Black Zero. Visiting the various planets which colonizing ships were sent, their searches for a new planet proved unfruitful, as each of the colonists sent to these various planets were found to have perished.
However, Zod and his followers took what they could from the remnants of their civilization, including a "World Engine" machine. When Clark activated the ship in the Arctic, it sent out a signal, which lead Zod to Earth. Zod claims that he intends to turn Earth into a New Krypton, but Clark is unwilling to go along with this plan since it will mean Earth's annihilation and the deaths of all humans.
Awakening from the vision, Zod tells Clark that with or without him, he will revive their civilization. As well, Clark's adjustments to the ship have made him no stronger than the other Kryptonians on it. This allows one of Zod's men, Jax-Ur (Mackenzie Gray), to obtain a blood sample from Clark.
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