Lois assists Clark in surviving his fall from the tower. Meanwhile, Chloe turns to the Helmet of Fate to find the missing Oliver, Tess discovers a deadly secret in a Cadmus laboratory, and Jor-El renders his judgment.
When Lois leaves for Egypt, Clark gets a new partner: reporter Catherine "Cat" Grant. he soon discovers that she's been targeted by an assassin who never misses. Meanwhile, Oliver searches for Chloe and Lois commiserates with archaeologist Carter Hall.
Radio shock jock Gordon Godfrey rises from obscurity to lead a campaign against the Metropolis vigilantes. However, Clark is busy dealing with the return of his cousin, Kara, who informs him that Jor-El has summoned her to Earth to deal with the coming darkness. Meanwhile, Godfrey threatens to reveal Oliver's secret to the world, leading Lois to take drastic measures to stop him.
Lois convinces Clark to attend his 5-year high school reunion. However, when they arrive a face from the past confronts Clark: Brainiac, now the heroic Brainiac 5 of the 31st century. he shows Clark images from the hero's past, present, and future to warn him what he will become if he gives into the darkness.
Lois is possessed by the spirit of Isis, an Egyptian goddess who seeks to reunite her dead lover's soul with his body... and bring forth Hell on Earth in the process. Meanwhile, Oliver glories in the revelation that he is Green Arrow, and Tess tries to help the heroes while tending to the young Lex clone.
Clark gets Lois out of town to cover a story so she won't risk herself at an antihero rally, but they find themselves in an isolated village where the townspeople plan to perform a yearly sacrifice... and Lois is their next victim. Meanwhile, Tess tries to cope with a rapidly aging Alexander as he begins to experience Lex Luthor's memories.
General Sam Lane and his daughter Lucy come to see Lois, and "protect" her from her newest boyfriend. Meanwhile, Rick Flag and the Suicide Squad prepare to take action as an anti-vigilante bill makes its way through Congress, and Oliver copes with Tess' new position at Watchtower.
A figure from Tess' past returns to haunt her, and she and Clark investigate a mysterious orphanage that hides a deadly secret. Meanwhile, Lois receives a tape made by her mother, Ella Lane, and after watching it decides to try reconciling Clark and his father.
General Slade is put in charge of the Vigilante Registration Act, and Oliver decides to sign up to determine what the government intends for registered vigilantes. Meanwhile, Arthur Curry begins destroying oil platforms with the aid of a beautiful young woman, and Clark tries to get his teammate to stop before he ruins the public's attitude toward vigilantes.
Tess discovers that Lionel left his heir a mirror box. When Clark accidentally activates it, he is transported to a twisted parallel dimension where Clark was raised by Lionel Luthor, who is still alive. Meanwhile, Clark Luthor has been transported to Clark's world, where he plans to escape his dominating father and conquer Earth.
As the Darkness spreads, citizens riot against heroes and Oliver Queen is their first victim. Meanwhile, the government moves in on vigilante sympathizers Tess, Emil, and Lois, Cat Grant must make a fateful decision, and Clark worries about his future relationship with Lois.
The VRA releases the captured heroes, who regroup and discover that they have all lost their powers, and remember Chloe Sullivan conducting medical experiments on them. The shock drives Oliver insane, and he receives a visitor... Chloe, who insists that things aren't what they seem.
Clark and Lois watch on television as Martha is shot while speaking at a anti-VRA rally. Meanwhile, Oliver and Tess discover that the parallel Earth's Lionel has taken control of the Daily Planet and LuthorCorp, and is grooming the Alexander clone as his new heir.
Chloe and Oliver inadvertently become involved with an FBI investigation into a serial killer, which leads them to Desaad, one of Darkseid's minions. Things take a turn for the worse when Desaad decides to recruit Chloe to his cause. Meanwhile, Lois prepares for the wedding and tries to convince Clark that he needs to create a secret identity.
Clark and Lois celebrate their bachelor parties, but wake up the next morning with no memories of what happened. As they trace back their steps, they discover that two of their party members are married, Lois bet away her engagement ring, Dr. Hamilton has rhythm, an armored car disappeared into thin air, and Clark has a pet lemur.
Tess reveals the existence of Alexander's superpowers to Clark and asks him to mentor the boy. Meanwhile, the Earth-2 Lionel plans to take control of the boy and unleash his dark side.
Clark Luthor uses his world's mirror box to come to Clark's world and trap his counterpart on the alternate world, where Clark is a pariah following the revelation of his identity and his weakness. While Clark-L attempts to turn Tess against his Lionel, Lois turns to Emil for help and Clark meets the alternate Jonathan Kent, a broken bitter man.
While Lois advises Clark to assume a bumbling, mild-mannered persona, a new hero arises in Metropolis: Booster Gold. Booster hogs the limelight and plans to usurp the Blur's role as inspiration to the city. Clark is more concerned with the fact that an alien weapon has gone missing, unaware that it has attached itself to a teenage boy, transforming him into an unstoppable juggernaut of destruction.
When Slade Wilson, banished to the Phantom Zone, mysteriously reappears, Clark plans a trip there to determine what is happening. Much to his surprise, Oliver goes with him and the two of them soon find themselves in the hands of the Zone's new ruler: Zod. Meanwhile, Lois discovers that Clark plans to sacrifice himself and confronts Tess.
Oliver searches for the Bow of Orion in hopes of finding a way to remove the Omega Brand and defeat Darkseid. Meanwhile, Clark takes Lois to the Fortress to seek his "father's" support for their life union, but Jor-El decides to temporarily Clark's powers and give them to Lois. However, Lois soon finds herself in conflict with the Toyman, who has gathered a team of villain to conquer Metropolis.
Clark and Lois attempt to make it to the altar, only to be plagued by doubts by each other's role in their lives. Meanwhile, the planet Apokolips approaches as Darkseid's prophets make Earth ready for his conquest of the planet, and Lionel abducts Tess as part of a scheme to bring back his son, Lex.