- The opening where Padmé's ship explodes, and we think that she has been killed from the impact. Then the pilot takes off her helmet, revealing herself as the real Padme. It doesn't lessen her anguish as she begs for her bodyguard Corde to stay with her. Corde merely says Sorry That I'm Dying before closing her eyes, and Padme stares with grief and horror. It's also the first time onscreen that we see the sacrifices that the bodyguards have to make by impersonating the queen.
- A Cry for the Devil moment: Zam Wesell gets injured and captured, and as a result Obi-Wan and Anakin interrogate her politely. They don't use any Jedi Mind tricks, just Politeness Judo, seeing that she's incapacitated, and then she gets killed in front of them as she's about to reveal her employer's name.
- The end where a 10-year-old Boba Fett is seen picking up his father's helmet.
- Jango's only fee (Aside from his considerable pay) for donating his DNA was having an unaltered clone. The novelization has Obi-Wan note that perhaps Jango only wanted a son, rather than someone to replace him.
- If you read the "Young Boba Fett" books, he (Boba) mentions that he thought that Padmé Amidala was exactly how he'd imagined his mother to be. The sight of him as such a young, innocent, idealistic child, and knowing what will happen to him in the future...
- Shmi Skywalker's death. She's been captured by Tusken Raiders, tortured to near death, and dies in her son's arms, just managing to get out "I... love..." before dying. Anakin's utterly broken plea for her stay with him complete with trembling jaw and watering eyes... Anyone who has ever lost a parent will know his sorrow.
Mace: What is it?Yoda: Pain...suffering...death, I feel. Something terrible has happened. Young Skywalker is in pain. Terrible pain.
- And what follows is a heartbreaking Roaring Rampage of Revenge as Anakin massacres the Raiders' village (including the women and children). And then, after that, he has a massive My God, What Have I Done? Heroic BSoD.
- Yoda's meditation of the whole affair beginning with Qui-Gon (probably the only person other than Shmi and Padme who had absolute faith in Anakin becoming a great Jedi) crying Anakin's name before screaming "No!" and fading away to Darth Vader's iconic breathing. Frank Oz's performance just sells the immense sorrow and concern he feels for Anakin.
- "Across The Stars." The credits version even more so, which segues into a mournful rendition of Anakin's theme from Phantom Menace before ending with the ominous bass strains of "the Imperial March."
- Obi-Wan, taken captive by the Separatists, is confronted with Count Dooku who tells him that he regrets Qui-Gon's death and would have liked them to work together. Obi-Wan retorts that Qui-Gon would never have joined up with Dooku. His tone and facial expression show that he's furious and that even after ten years the loss still hurts like hell. So much for no attachments, ey?
- In a Deleted Scene, while visiting Padme's parents Anakin finds a photograph of Padme doing intergalactic community service. She tells him she was helping to save a species named Shadda-Bi-Boran from their own home planet whose sun was dying, and that they "were" wonderful. When Anakin asks, "Were?" she somberly tells him that the species couldn't live off their planet and eventually became extinct, meaning her work was All for Nothing. Yet she kept doing that work, despite the losses, until she became queen.
- Also from the novelization, Padme notes that the Separatists are an Ungrateful Bastard lot for how she plead for mercy on their behalf, despite the fact that they invaded her planet and enslaved her people, and to return the favor they've tried to kill her. It doesn't even make sense from a Pragmatic Villainy standpoint to eliminate an opponent that prefers clemency to violence. Granted, Palpatine was manipulating them to assassinate Padme since she opposes his rapid rise to power, and probably played on the Separatists' emotions.
- Meeting Owen and Beru as a polite young couple, hospitable to and concerned for the stepbrother they've only just met ... and knowing all along that they're Doomed by Canon to be murdered on his orders.
- That sweet kid from The Phantom Menace has been unwittingly under Public Enemy Number One's influence the past ten years—and Public Enemy Number One has cultivated borderline personality disorder in him.
Tear Jerker / Attack of the Clones