Lex Luthor's ex-wife comes to town determined to revenge the fall of her ex-husband. The target of her revenge is Lois Lane and Superman who in her mind is the two foremost responsible for the fate of Lex Luthor. With her she brings an impostor who through plastic surgery looks exactly like Lois.
Lois gets a bit jealous and insecure after Clark is nominated for a journalism award and she is not. A villain using sound waves as a weapon, is trying to extort the city of Metropolis for half of the money in its banks.
Lois fights a hard struggle to protect one of her sources. When it looks like the source has been murdered as a result of having provided Lois with information Perry feels he has no choice but to suspend her. After some encouragement from Superman it now becomes Lois mission to solve the murder and find out what really happened.
Lois starts to receive gag gifts from a "secret admirer." She and Clark begin to investigate these pranks and discover that behind them is a man who Lois helped send to prison 5 years earlier. He is now out of jail and looking for revenge.
While visiting Lois' Uncle Mike, she and Clark witness gang intimidation and discover that "Intergang", a new criminal organization has moved into and begun to control south Metropolis. Superman becomes powerless to help because of their threats against everyone closest to him. Lois gets jealous when the investigator in charge, Mayson Drake, begins to show interest in Clark.
A general is killed at a demonstration of the army's latest weapon, by that weapon. As Lois and Clark investigate they discover a terrorist plot to high-jack a satellite and that the person behind the plot just might be Lois' best friend from college and her supposedly dead boyfriend.
A scientist who believes he can alter people's personalities using their DNA brings Bonnie Parker, Clyde Barrow, John Dillinger, and Al Capone back using a special cloning process. When Clyde shoots Clark during a confrontation, he must fake his death in order to hide his dual identity.
Superman is struck by lightning while stopping William Wallace Webster Waldecker from committing suicide and his powers are copied into Waldecker transforming him into Respendantman. Superman must now contend with figuring out how this happen and teaching the newest superhero how to use his powers responsibly. Meanwhile, Dr. Gretchen Kelly, Lex Luthor's doctor, witnesses the power exchange and becomes obsessed with getting powers for herself.
After Mr. Schott is fired from his toy making job, he decides to get revenge and make a lot of money by creating Atomic Space Rats, which spray a substance that causes everyone to be more greedy. It also makes adults, including Clark, act like children.
Lucy Lane moves back into town with her boyfriend Johnny. After Johnny is shot by police during a robbery attempt, two scientists transform him into a cyborg that is powered by Kryptonite. After he discovers this he decides to use his new powerful body to be a more prolific criminal and try to defeat Superman.
After Perry's men's club is robbed and all his savings taken, Lois and Clark begin to investigate and find that the same martial arts expert who robbed the club is responsible for several other robberies. The thief uses special power totem bracelets which allow them to use Superman's strength against him.
Dr. Faraday creates a device that can transmit information to someone's brain through a beam of light and uses it on Lois before he's killed. Two scientists, who are trying to get their hands on the device, make Superman blind with a beam of light shone into his eyes. Lois takes care of him at her apartment, while everybody thinks that Clark is in the mountains with Mayson Drake.
Clark finally asks Lois out on a date, which she accepts after thinking about it for a while. But before they can go out on their first date, Dr. Gretchen Kelly brings Lex Luthor back to life and he begins to work toward getting back his fortune and Lois, by force if necessary.
Television news reporter and Intergang assassin, Diana Stride, decides to find out and expose Superman's secret identity. At the same time, her former partner, Mr. X, decides to turn states witness and she is attempts to silence him before he can name her. Clark must try to protect both himself and Mr. X from her deadly games.
Kyle Griffin (a.k.a. The Prankster) escapes from jail using a new weapon that freezes people using a yellow beam of light and resumes harassing Lois. This time he has an added goal: kidnapping the President while he is visiting Metropolis.
Lois and Clark meet H.G. Wells, who has traveled on his time machine with a companion from the future. This companion named Tempus roams the city robbing people of gold, which is needed to fuel the time machine. Wells tells Lois and Clark that future's Utopia was founded by Superman descendants. Tempus wants to destroy Superman, because he finds the future boring. Tempus kidnaps Wells, as he doesn't know how to use the time machine himself. Wells is supposed to take him to 1966 Smallville, where infant Kal-El arrived on Earth. However, they travel to 1866 and not 1966...
Superman is forced to get a lawyer when someone he saves sues him for damages incurred during the rescue. Lois discovers a secret about Dan Scardino's livelihood, and she and Clark decide to have a romantic relationship.
Clark is ready to tell Lois that he's Superman when he is interrupted by Jason Mayzik who has obtained a diary written by Tempus which reveals, among other things, that Clark is Superman. Mayzik kidnaps the Kents who are in Metropolis to celebrate their anniversary, and blackmails Clark into stealing $20 million in diamonds from Mayzik's brother's jewelry store. Mayzik is also working with Lex Luthor's former accomplice, Nigel St. John, who has the Kryptonite that he took from Lex, so that he can kill Superman. Clark robs the diamonds but Lois, who had followed him, ...