In the collapsed dam, Lois encountered Philipe Lamont, the boy previously possessed by Bizarro while trying to escape. Clark heard her calling for help and took all three to the hospital where the doctors tried to revive Chloe. Restless, Lois instructed Clark to stay with Chloe while she went to the Luthor Mansion to search for clues that pointed to Lex's involvement with the project. There, she ran into Bizarro, who had taken Clark's form. Mistaking him for Clark, she was angered when he made a pass at her and slapped him across his face. Later, Lois deduced that "Clark"'s odd behavior was due to his grief over Lana Lang's reported death, and sincerely offered her condolences.
Lois was determined to investigate the dam and after discovered a red spaceship with Clark, she took a picture with her cell phone but it was crushed by a blonde woman, who knocked Lois out. Lois visited Chloe at work at Daily Planet and tried to convince her that she'd seen a UFO but Chloe refused the idea. Then the new editor of the newspaper offered Lois a job if she could write a good story about her spaceship. Although Lois wrote her story, but had no photograph to accompany it, so Grant declared that he would not publish it, but would still hire her at the Daily Planet.
Lois became Grant's ingenue, getting sent on prestigious and exciting out-of-town assignments. However, she was still interested in proving Lex Luthor's role in the Reeves Dam project.
Against Grant's assignments, she chose to investigate the purchase of land close to the dam, authorized by someone with the initials "LL". She sneaked into LuthorCorp but was quickly caught and thrown out by Lex Luthor. Grant asked Lois to accompany him to a social function, but she turned him down. However, Lois and Grant became increasingly close.
Lois was casually visiting Grant in his office when they were suddenly interrupted by Lana, who had stolen evidence of Lex's projects and demanded they print the story. When Grant refused to do so, Lana assaulted him and Lois tried to fend her off but Lana threw her through a glass door, knocking her unconscious. After recovering at the hospital, Grant brought her flowers and tried to warn her off the Luthor story. Lois acknowledged their growing attraction, but she refused to back off.
Lois and Grant finally began a relationship while she continued to cover big stories for him. They were unwittingly seen making out by Chloe, who was furious that Lois would endanger her own career by having a relationship with Grant. She warned Lois to break up with Grant, and Lois attempted to do so, but ultimately, she and Grant agreed to continue their relationship but keep it a secret.
On Christmas, Lois was assigned to write an exposé on Lex but that same day at work, Lois received a call of a man that manipulated Lois into following out his orders to write an article about Lex projects by placing a bomb on Chloe and trapping her in a non-functioning elevator. The caller revealed himself to be Adrian Cross and told Lois he was a clone created by Lex. He directed her to enter the interview wired and armed, but she was unable to force a confession out of Lex before he knocked her unconscious. As a result, Lois missed the revelation that Grant Gabriel was a clone of Lex's dead infant brother. Later, Gabriel visited Lois at her home. Sure she was going to be fired. Lois want to continue dating, but Gabriel suggest that it was a bad idea for them to work and date at the same places, Gabriel decide to broke up with Lois.
Shortly afterward, Lois discovered Oliver had returned to Metropolis and went to the Queen Tower to confront him. They were attacked by a female vigilante hired by Lex to kidnap Green Arrow and then Lois learned that Oliver was Green Arrow. When Clark and Chloe rescued her, she tried to keep Oliver's identity a secret but was surprised to find out that they already knew. Before he left town again, Oliver asked if they might try to make it work, but Lois was unwilling. She later tearfully confessed to Clark that she loved him, but would not be able to handle his greater cause and would always resent being left behind. Clark offered his support and they exchanged a solemn hug.
Lois started researching about the death of Patricia Swann, with Jimmy Olsen as her sidekick. The two later went undercover as janitors to see how Lionel Luthor was involved. Lois and Jimmy later discovered that Lionel went to see Lana at the Isis Foundation, and they learned that Lex was behind the murder of Patricia, not Lionel.
As Clark and Chloe were working on a search for Brainiac, Lois rushed in to inform the two about Lionel Luthor committed suicide by jumping from his office window. Lois and Jimmy found a picture of Lionel being pushed from his office window. When they went to go to the Isis Foundation, they were caught by Lex’s assistant and held at gunpoint by her. Lois was shot for trying to stop her, and was placed in a freezer with Jimmy to make sure they don't expose Lex for murdering his father. Clark used his heat vision to keep them warm to prevent them from dying of hypothermia.
After Lana went in catatonic state, Lois tried to support Clark and help him with Lana's condition as he helped her when she had to break things off with Oliver.
Lois suggested Clark apply for an internship at the Daily Planet, saying that he's meant for more than farm work. He refuses the offer and tells her that he can never work for Lex Luthor. Then she asked him about his and Lex’s past friendship and how that lasted for so long because they had nothing in common with one another, but Clark just said that sometimes people don't turn out to be who you expect.
Lois then began digging into Lex's excursions to the Arctic Circle, but Jimmy was set up by Lex to throw her off the track. She believed Jimmy, but was still skeptical about Lex's activities. Lois arrived at the Kent house just as Clark finished viewing a break-up video left for him by Lana Lang. She offered support by giving a devastated Clark a comforting hug.