The second season of Smallville, an American television series developed by Alfred Gough and Miles Millar, began airing on September 24, 2002, on The WB television network. The series recounts the early adventures of Kryptonian Clark Kent as he adjusts to life in the fictional town of Smallville, Kansas, during the years before he becomes Superman. The second season comprises 23 episodes and concluded its initial airing on May 20, 2003. Regular cast members during season two include Tom Welling, Kristin Kreuk, Michael Rosenbaum, Sam Jones III, Allison Mack, John Glover, Annette O'Toole and John Schneider. Glover, who was a recurring guest in season one, was promoted to regular for season two. At the end of season one, Eric Johnson, who portrayed Whitney Fordman, had left the series.

Season two picks up directly where season one ended, with Clark (Welling) dealing with the aftermath of the tornadoes that hit Smallville. This season, Clark finally learns who he is and where he comes from, but must also acknowledge a potential destiny set into motion by his biological father that could change his life and the lives of those around him forever. Clark's relationship with Lana Lang (Kreuk) becomes increasingly closer, straining his friendship with Chloe Sullivan (Mack). Clark's best friend, Pete Ross (Jones III), learns Clark's secret this season.

Before the start of the second season, Gough and Millar established a writing staff to help develop episode stories for the show, which eventually saw the introduction of two characters that would shape Clark's life, Dr. Virgil Swann and Clark's biological father Jor-El. These roles were filled by Christopher Reeve and Terence Stamp, respectively, who were previously known for their respective roles as Superman and his nemesis General Zod in the Superman film series. Special effects company Entity FX became the primary effects unit for the show this season, winning awards for two of the episodes they worked on. Apart from the digital effects team, the series and its actors were nominated for and won various awards as well. Season two performed better than the previous season, averaging 6.3 million viewers a week, and placed #113 in the Nielsen ratings, up from #115 the year before.

At the start of the second season, Al Gough and Miles Millar brought in Ken Biller to run the newly formed writers' room. For the first season, Gough and Millar usually wrote the final draft of every episode because they were still seeking the show's voice. The pair understood that a writing staff would help "expand [the] show". As part of their expanding, they also brought in comic-book writer Jeph Loeb, who spent his first two weeks seeking fresh ideas for new episodes. One of the decisions the new writing team came up with was letting Pete in on Clark's secret. The decision to let Pete learn Clark's secret was a choice made so that the character would have a function on the show, and allow Clark someone who was not one of his parents. It was also a way to examine the "power of friendship and loyalty", and "the price of having to keep a secret".

Not all of Smallville's stories this season came from the writing staff. Mark Warshaw, who was head of the internet team that wrote the online Smallville articles for the Ledger and Torch, which interwove the television episodes with online, fictional newspapers that continued the stories from the show, was the one that came up with the idea behind "Skinwalker". Warshaw's story was about a Native American girl who falls in love with Clark, while at the same time revealing Clark's destiny to him. The story was bought and given to Kelly Souders and Brian Peterson on the writing staff to work on a screenplay. The episode had a significant role in the series, as it introduced the Kawatche caves—which held the Kryptonian language written on its walls—and explored Clark's origins, while at the same time posing the question that people from Clark's homeworld may have visited Smallville before Clark arrived on the planet.

For the second season, Gough and Millar brought in Christopher Reeve, who portrayed Superman in four feature films, as a guest star for a pivotal role in Clark's life, that of Dr. Virgil Swann. The pair always had intentions of bringing Christopher Reeve onto the show, and when they found out that he enjoyed watching the show himself Gough and Millar decided that they were going to bring him on for season two. They had already crafted a character, Dr. Virgil Swann, they knew would reveal the truth about Krypton to Clark, and they decided that Reeve would be perfect for the part. Gough and Millar believed it was "natural" for Reeve to be the one to educate Clark about his past, and help him see his future, and the scenes between Reeve and Welling have been described as a "passing of the torch" moment for the series. Along with Reeve, another actor from the Superman films to be brought into the show was Terence Stamp, who portrayed General Zod in the first two Superman films. Stamp's role as Zod in the films, coupled with how the writing team portrayed Jor-El's early appearances—giving Clark a message that he will rule Earth with strength—led to fan theories that Jor-El was in fact General Zod at the ComicCon that met two months after the episode aired. Gough assured the ComicCon audience that the character was Jor-El, and not Zod in disguise.

In addition, Jeph Loeb requested the introduction of Superman's future ally, Metropolis Police Lieutenant Maggie Sawyer, for the episode "Insurgence". As Loeb recalls: "Ken [Biller] had written a hard-bitten, crusty kind of cop. I asked him if he minded if it was a woman, and explained who Maggie Sawyer was and the role she would play in the future". The concept for "Insurgence" also developed from an aspect of the Superman mythology that stemmed back to Superman's original incarnation, which was his ability to leap tall buildings in a single bound. After their Thanksgiving break, the Smallville writers were in the writers' room when Miles Millar walked in and exclaimed, "I think it's time for Clark to leap a tall building". Jeph Loeb and the other writers had already been trying to develop a story that involved a hostage situation, and after Millar made his announcement the team suggested that they also pay homage to the Bruce Willis action film Die Hard. The setting for the hostage situation was LuthorCorp Plaza; the team introduced the "Daily Planet", another pivotal piece of Superman lore that would one day employ Clark Kent and his alternate identity of Superman, by using it as the building that Clark uses to execute his "first leap". "Insurgence" was actually written before "Visage" and "Suspect", but not filmed until after both of those episodes because the team was having difficulty figuring out the logistics of producing the episode. Afterward, the episode would be scheduled to air between "Visage" and "Suspect".

This season also saw the introduction of red kryptonite. In the fourth episode of the second season, titled "Red", Clark buys a high school ring that contains a red kryptonite gem. The effects of the kryptonite were meant to act as a metaphor for drugs. Loeb was given the task of writing "Red" by Gough and Millar, and one of the things he decided on was that the ultimate pay off with the kryptonite would be Clark finally kissing Lana. As Tom Welling describes it: "With 'Red Clark' he's completely aware of the consequences of his actions at the time, but he doesn't care! He doesn't care what happens to you, and he certainly doesn't care what happens to himself, because he probably realizes that nothing can happen to him. It's always fun to be that way, even in real life, because we're not allowed to be that way all too often". One of the concerns for the episode was whether the audience would embrace the idea of a "bad Clark", as Ken Biller knew that Clark would have to be "the villain of the story", but audiences did embrace the idea and after the good ratings "Red" received, the WB requested more episodes with red kryptonite. In contrast, Gough and the crew did not like using it because of the idea of "Clark [turning] bad", but the team asked themselves, "what if a friend slips something in your drink and you don't know it?" This became the basis in "Rush", where Pete slips a shard of red kryptonite into Clark's pocket; it also gave the network what they wanted, but in the form of a single act instead of the entire episode. This element would show up again in the season finale, when Clark slips on another red kryptonite ring before riding out of Smallville on a motorcycle. According to Ken Biller, the moment Clark goes searching for the kryptonite is the payoff they had wanted with that piece of Superman mythology. The show had established that red kryptonite removes Clark's inhibitions, and in the season finale, Clark is to the point that he is willing to "go 'on drugs' to solve his own pain and [...] guilt about what he's done".