WARNING: Spoilers are unmarked.
Season 1
Episode 1: Pilot
- Jonathan Kent's death in the opening montage. He's walking through Smallville with Clark and Martha as they help the town prepare for the Harvest Festival, only to suddenly collapse from a heart attack in the middle of the street. It's especially sad with Jonathan's proximity to Clark in this version; he was right next to him, and this time, Clark was truly, utterly powerless to save his father.
- Clark is clearly struggling to connect with Jordan, and he fears that he's going to lose him if he can't make a connection soon.
- Shortly after Clark finds out that he's been fired from the Daily Planet, he receives a phone call from his mother—or rather, from her doctor using his mother's phone. Before she can even finish telling him what's wrong, he immediately abandons his conversation with Lois and runs/flies all the way over to Smallville. Yet even as fast as he can go, he can't make it back before Martha dies of a stroke, hearing her last words to him: "Come home."
- Watch as he slowly approaches Martha's room. He's not only hesitant to see her body; he's desperately honing his super-hearing to detect her heartbeat, only to concede that she's truly gone and finally faces her.
- After Jon and Jordan find out the truth about their dad, a very upset Jordan tells Clark "You may have been sent here to be some hero, but you sure as hell weren't sent here to be a father." This clearly hurts Clark more than Kryptonite ever could as he's seen in the next scene horrifically wondering if he's a bad father.
- In an instance of Fridge Sadness, Clark not running over to the barn after Jordan and Jonathan's accident. He has Super-Speed, but there are witnesses around, so he has to pretend to be slow when all he wants to do is run to his sons and save the day.
episode 2: Heritage
- Lana admits to Sarah that she's a Stepford Smiler and is clearly feeling immense guilt about forcing her daughter to try to hide her pain as well.
Episode 3: The Perks of Not Being a Wallflower
Episode 4: Haywire
Episode 5: The Best of Smallville
- Irons meeting Lois who, according to him, is exactly the same as her counterpart from his Earth. He gives a Longing Look as he secretly watches Lois and Clark lovingly embrace each other and walks off. He says she's exactly the same as his Lois back in his world, except "she married someone else".
- The irony of the fact that he doesn't know that Earth-Prime Lois is married to the man who murdered her on his Earth and destroyed their planet; whom he's trying to kill to avenge her and his homeworld.
episode 6: Broken Trust
- Jordan telling Lois how his powers just alienate him even further from everyone. He tells her how guilty he feels over breaking Jonathan's arm, whose bones he can still hear snapping, as well as having to lie to his only friend Sarah. When Lois pulls him in for a hug he immediately bursts into tears, just wishing for it all to end. Then his Super-Hearing kicks in and causes him to have a seizure.
episode 7: Man of Steel
- Irons and his daughter Nat watch Lois be brutally murdered by Superman on a live news broadcast.
episode 8: Holding the Wrench
- Jonathan looking through pictures of Irons' daughter Nat, who's (technically) his biological half-sister. He is saddened he didn't get to meet her and comments that she "seemed cool".
- Lois's outburst towards Jonathan when he is almost killed by Irons' truck's AI.
- Lois crying while expressing to Dr. Wiles how scared and helpless she felt when Jonathan was in danger. While it doesn't really excuse her outburst, it does remind the audience that Lois is a mother who truly cares for her children and worries about them constantly.
- The Reveal that Lois had a miscarriage. Even worse, Lois intended to name her "Natalie" after her grandmother, the same name as Irons' daughter. Her heartbroken line to her therapist, "I was so excited to meet her..." really just guts you in her clear grief of losing her child (and the daughter she dearly wanted and was excited to have).
Episode 11: A Brief Reminiscence in Between Cataclysmic Events
- In flashback, after years of training with his powers, Clark finally returns to Smallville. He seeks out Lana, seeing her outside a theater and ready to go to her... only to see Kyle coming up, the two hugging and Clark using his vision to see the engagement ring on Lana's hand to realize it's too late for him. Giving one last Longing Look, he simply walks away in newfound heartache.
- Tal-Rho destroys Jor-El’s consciousness. He only has time to say “I love you, son” before being destroyed forever before Clark’s eyes.
- Even worse, after losing Martha in Episode 1, Lara in Episode 10, and Jor-El here, Clark has lost all three of his remaining parents in the span of a few months. Trauma Conga Line barely begins to describe it.
Episode 15: The Last Sons of Krypton
- John admits he can’t stay with the Kents because seeing Lois reminds him too much of his Lois that he loved and lost. It simply hurts too much to see the love of his life happy and in love with someone else, even if it's not technically his Lois.
- The Kents have a funeral for Jor-El, with Clark giving a stirring eulogy about how while everything Jor-El told him about his powers and his homeworld was important, all of that paled in comparison to Jor-El simply being his Dad.
Season Two
Episode 2: The Ties That Bind- Sarah reveals why she's been distant with Jordan. She explains that, while at camp, she shared a kiss with a girl. She tries reassuring him that it didn't mean anything and "just happened", but the heartbreak on Jordan's face at being cheated on by the girl he loves (and was so excited to see after being a month apart) is hard to watch. She tries reaching for him, but a heartbroken Jordan backs away from her and simply leaves.
Episode 6: Tried and True
- With the reveal of his affair, Lana and Kyle's marriage is crumbling. Kyle gets down on his knees, professing his love for her and their girls, but Lana, despite how much it hurts to do so, kicks him out of the house to give her heart time to heal.
- Jordan learning Jon's powers aren't natural, but from huffing X-Kryptonite. He was so excited to share his experience with his big bro, only to have these hopes smashed to pieces.
Episode 7: Anti-Hero
- Jonathan having his fallen moment. He's on the verge of being kicked out of school and Lois, already on edge with what's happening, reads him the riot act. But it's Clark, who already went through the wringer with the events of the episode and now learning what Jonathan did, is what causes Jon to break down into tears. It's bad enough being scolded by your parents, but when one of your parents is Superman, the scolding is even worse.
Episode 8: Into Oblivion
- The look on Clark's face when Natalie talks about John possibly having brain damage or a tumor. It may not be his fault what Bizarro did, but you can bet he still feels the guilt.
- Kyle and Lana's awkward conversation when he comes to pick up Sarah. Both of them really want things to go back to normal, but it's unclear if they ever will.
Episode 10: Bizarros in a Bizarro World
- Anderson comes face-to-face with Bizarro's family, and is horrified to realize that the man he killed was a husband and father... and by extension, realizes that Superman is a husband and father. His subsequent Heel Realization absolutely devastates him, and when he tries to apologize to the El family for killing their patriarch, the words all come out garbled because of the change in realities.
Episode 12: Lies That Bind
- Lana learning Clark's secret...and reacting as a typical person would to learning that her childhood friend and high school boyfriend and his wife had been lying to her for years.
- Lana realizing that the accident she and Pete Ross were in was the first time he used his powers to save someone and Clark explains that the reason he left the next day was to go on a Journey to Find Oneself. When she asks why he never came back until now, Clark reveals that he had once before only to discover she was engaged to Kyle.
- Lana accusing Lois of using her and asking if they were genuinely friends only for Lois to reveal that due to her background, she didn't have many friends if any and so yes, they are genuinely friends.
- Lana ultimately deciding she needs some time and cuts the Kents out of her life as she realizes she must now lie to her family and friends while dealing with the knowledge of a potential major threat.
Season 3
Episode 1: Closer- Sam Lane invites Nat out to see a movie, ostensibly to bond with her, and then turns around and tries to pitch the idea of her going to the D.O.D. Academy. Nat is genuinely hurt at the idea that he only invited her out to recruit her, especially since she had already told him that his alternate-universe self was her grandfather.
Episode 2: Uncontrollable Forces
- Lois convinces a suicidal Judge Reagan that she knows what it's like to fear death... because she just found out that she has stage-3 breast cancer. And that happens to be the exact moment that Superman flies in, just in time to overhear her.
Episode 3: In Cold Blood
- This episode shows Lois telling her father about her cancer. Sam Lane—who, throughout the rest of the show has been incredibly tough and strong—actually breaks down crying at the table as he absorbs the news that his beloved daughter is ill.
Episode 5: Head On
- Clark talks to a pair of cancer patients, who tell him bluntly that chemo is not fun and he's going to have to get accustomed to seeing Lois in pain. When one of the patients nods off, the other tells him about how she's been on both sides of the cancer experience; before developing cancer herself, she watched her daughter succumb to the disease... in the very same chair in which Clark is now sitting.
- Throughout the season, we see how difficult it is for Clark to face a problem that he can't simply punch out. As Superman, he's used to facing natural disasters, villains, criminals... physical dangers that he can deal with. This, however, is one he can't fight, can't save Lois from, can't use superpowers or his investigative skills to solve. All he can do is offer support.
Episode 10: Collision Course
- A fairly big one comes as Kyle's girlfriend, wife, and daughter all lie to his face about there being someone superpowered in Smallville. Understandably, he's furious and upset.
- The governer of the state, meeting with Lana, asks if her ex-husband ran off with some young floozy...while Chrissy is right there.
- After Sarah and Jordan have an argument (she's upset with him for being rude to Junior, he's upset with her for brushing him off), he bitterly tells her that sometimes he regrets having fallen in love with her.Sarah: So do I.
