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Tear Jerker: Star Wars: The Clone Wars
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"The Hidden Enemy", when it's discovered that one of the Clone troopers, Sgt. Slick, betrayed the Republic. And in a way, he was justified. With the Jedi using the clones as fodder in the war, he was desperate for a way out. Even then, his last words felt genuine.
"I- I love my brothers. You're too blind to see it, but I was striking the blow for all clones."
Truth enlightens the mind, but won't always bring happiness to your heart.
Hevy'sHeroic Sacrifice in "Rookies". Doubly so in the season three premiere, Clone Cadets (Season Three, Episode 1). During training, Hevy befriended a clone assigned to maintenance duty named 99. When his teammates end up back on Kamino, they have to tell 99 that he died.
The ending of Downfall of a Droid, where now nobody cares and forgets about Artoo (because he's assumed destroyed in action), except for Anakin.
To some, the death of Nhadar Vebb in The Lair of Grievous. Kit Fisto's reaction in which utters, "No...", is especially depressing.
Ahsoka becoming depressed after losing 8/10 of Blue Squadron (though they say it was the whole squadron, but there were 2 survivors besides Ahsoka) in Storm Over Ryloth, made even worse that it was her fault because she disobeyed Anakin.
In Innocents of Ryloth when the twi'lek girl, Numa shows the soldiers what used to be her home.
And to top it all off, she starts crying when Waxer finds her doll and gives it to her...
Cut Lawquane's backstory and what led him to deserting the clone army.
Anakin's reaction to Commander Ponds' execution by Aurra Sing
Anakin: That was Ponds....
Onaconda Farr's death in Senate Murderers. Especially the funeral.
The last stand of the Republic in "Supply Lines". Especially crushing is Ima Gun-Di's last stand with Captain Keeli, and his last words "The Twi'leks will live to fight another day" as he's finally overwhelmed.
When Kamino is attacked, 99 does everything he can to help the clone troopers survive, eventually getting gunned down while trying to get more grenades in the middle of a firefight.
Mina Bonteri (A member of the CIS civilian government and Padme's friend) getting killed off for advocating peace. Just another of the senseless sacrifices of war. One has to wonder what happened to her son, Lux, after her death.
We find out in "A Friend in Need" (Season Four, Episode 14), where he leaves the Seperatists and wants revenge on Count Dooku.
Count Dooku being forced to have Asajj Ventress killed in "Nightsisters". And the reveal of Ventress's full backstory is just as bad.
It's worse in "Massacre" (Season Four Episode 19), when her home planet is, well, massacred.
From the same episode, Ventress outright begging Mother Talzin not to leave her alone.
The newly brainwashed and transformed Savage Opress killing his brother Feral as a test of loyalty to Ventress and Mother Talzin. Also doubles as Nightmare Fuel.
The Mortis Trilogy rolls out these throughout:
Anakin seeing his mother again in "Overlords" when it turns out to be The Son of Mortis impersonating her.
In Ghosts of Mortis, Anakin (now controlled by the Son of Mortis) now knows he will murder Obi-Wan (as well as many innocents) in th near future. When the pair face off Anakin destroys Obi-Wan's transport in order to keep him stranded on the planet, telling him that he's only doing it to keep him safe, "for his own good". Well, we all know how that turns out...
Obi-Wan's face when he sees dark Anakin.
The Son of Mortis, while retrieving the Dagger of Mortis from the Daughter's tomb, tells his deceased sister that he truly did care for her. Also counts as a Heartwarming Moment.
Son: It's ironic, my sister. You were the only one I truly loved...
The Father committing suicide to take the Son's power away from him and the Son dying in his father's arms after Anakin mortally wounds him.
It gets worse. It turns from a Heroic Sacrifice into a Senseless Sacrifice because instead of keeping Grievous as a prisoner, they end up having to give him back to the Separatists in exchange for Anakin Skywalker, who was captured by Dooku shortly after Grievous's capture.
The Umbara rolls these out one after another in the latter two episodes.
The death of Waxer. Made all the more tragic because he was killed by his own brothers as a result of Krell manipulating two squads of clones into fighting each other. As a final jab, there's a smiling picture of Numa painted on the side of his helmet.
Live to fight another day, boys! Live to fight another day...
Ahsoka's final scene in Slaves of the Republic has her being tortured by Atai Molec after trying to fling him off a ledge while caged above the queen's palace and he continues torturing her as the scene wipes to the slaver ship carrying Obi-Wan arriving at Kadavo, while we hear her screams of torture echo out. Made even more tragic that it was the last shot of her in the first half of Season Four, and that we would not find out if she will be saved until January 2012. Truly, one of the most heartbreaking moments of the series.
Obi-Wan's "funeral", especially Satine's reaction. While any Genre Savvy viewer (or anyone who's seen Episode III) would realize that Obi-Wan isn't actually dead, Satine genuinely believes that the man she loves is dead and seeing her break down crying, particularly after she has spent every other episode she appeared in keeping up a strong, unflappable appearance, is heartbreaking.
Also a bit earlier, seeing Ahsoka barely holding her tears and at the same time, hearing Anakin's desperately calling out Obi-Wan's name, trying to wake him.
Anakin vs. Rako Hardeen, who is actually Obi-Wan in disguise in "Friends and Enemies".
The end of "Massacre", where all of the Nightsisters (excluding Ventress and Mother Talzin) are killed, with Ventress' reaction selling it.
If you look at the scene more closely, you'll notice that it almost mirrors Obi-Wan and Qui-Gon's battle against Maul in Episode I. In this, Maul finds himself watching helplessly as his brother fights Sidious alone which ends in his death, putting Maul in the very same position as Obi-Wan over a decade before when Qui-Gon was killed. Seeing the devastated look upon Maul's face, it's almost as if he finally understands the pain he put Obi-Wan through when he killed Qui-Gon.
One has to feel for Ahsoka at the end of "The Jedi Who Knew Too Much". In probably less than a day, her entire life was ruined by someone (a Force user) setting her up for reasons she can't comprehend, and even her master hasn't (from her point of view) done much of anything to help her.
Then there's Anakin. Ahsoka is practically his daughter/little sister, and he's unable to help her in any way other than convince her to come back with him. Just seeing him trying desperately to find her is enough to make anyone tear up, especially when you consider how badly Anakin reacts to losing his loved ones.
And then there's Rex. When he's issuing Anakin's orders, his tone of voice makes it obvious just how shocked he is by the turn of events.
In the final episode of Season Five and the series, The Wrong Jedi, The horror on Anakin's face just screamsMY God What Have I Done, as he realises that Ventress is right about comparing how the Council abandoned Ahsoka, to how Dooku did the same to her. Also the compassion and blame in the once psychotic Nightsister's voice as she explains this.
The what makes this episode almost unbearable is that Barriss is right. The Jedi are fighting a pointless war in the name of a Sith Lord, (albeit unknowingly) and the Republic that they have fought so hard to protect will soon cease to exist. You can tell by Palpaten’s expression that her speech strikes a nerve.
Barriss: This republic is failing! It's only a matter of time.
The ending of "The Wrong Jedi", where Ahsoka leaves the Jedi Order, even after her name is cleared, because her faith in the Order is so shaken that she can't bear to stay.
The last shots of Ahsoka's face as she leaves the Order take it to an entirely different level: the always cheerful, optimistic and enthusiastic girl cries without hiding.
The fact that Dave Filoni kicked everyone out of the recording studio except for Matt Lanter (Anakin Skywalker) and Ashley Eckstein (Ahsoka Tano) to record this scene further shows how powerful it is.
Ahsoka's look of shock upon learning that Barriss was the one who orchestrated the whole plot. One can only imagine what Luminara's reaction would be, seeing as her once-model apprentice has fallen to the dark side.
And even before that, she's totally despondent while sitting in a Republic jail cell, pretty much convinced that she's doomed because Anakin is the only one actually trying to help her (not that she faults Padme for defending her, mind you, she's just quite convinced it's pointless).
The ending credits also qualify. Instead of the usual circle wipe and ending theme, the scene just fades away and a rather somber version of Ahsoka's theme plays through the credits. Cartoon Network didn't even do their usual picture-in-picture credits advertisements.
Doubles as a meta-example, as this not only marks the end of he end of the series (at least on television), as Disney said "no" on continuing it (Even though allegedly Lucasfilm Animation is continuing production on new Clone Wars story arcs, but how they will show them is currently unknown), but also marks the end of Lucasfilm's collaboration with Cartoon Network, as future Star Wars animated programs, including the upcoming Star Wars: Rebels, will be airing on Disney XD or Disney Channel.
Season 6/Bonus Episodes
The whole Order 66 Arc. Let's see:
Tup's fate. He had absolutely no control over his actions (killing a Jedi master) and for that he got drugged, restrained and was prepared to be killed and dissected by the Kaminoans (who are revealed to be part of the Sith conspiracy). Then Fives and his Robot Buddy, in the course of trying to save him, discover the reason behind all of this... only for Tup to die anyway since he was weak to begin with. Oh, but you think it ends there? Ha ha, no. It just gets worse.
Fives is taken back to Coruscant to reveal what he knows... to Chancellor Palpatine. I think you can guess where this is headed. Having been drugged by Nala Se beforehand, Fives can't properly convey what he knows and grows ever-more paranoid while being hunted for trying to assassinate the Chancellor, who revealed the entire plot to him. Finally, he's gunned down by his fellow clones while reaching for a weapon.
Then there's his Famous Last Words to Rex. Even Commander Fox and the Coruscant Guard (who were the ones who gunned Fives down) are saddened by this and take off their helmets in respect.
And what would've become of a deserter like Cut Lawquane? Not to mention his adopted family.
Fridge Horror wise, what may have happened to AZI-3, the main source of comic relief in this otherwise dark story arc? Considering that he was involved in helping an allegedly "defective" clone rebel against the Kaminoans, he was most likely deactivated or memory-wiped sometime after Fives went back to Coruscant.
Then there's Rush Clovis's ultimate fate as it were. All he wanted to do was purge the Intergalactic Banking Clan of corruption and keep it a neutral party as it used to be. Then after getting aided by Count Dooku in finding the stolen accounts and coming to power, Dooku blackmails him into "favoring" the Separatists and then sends an invasion fleet to Scipio to make it look like he's abusing his power. In the end, he inadvertently brought war to Scipio, deliberately fell to his death to let his beloved live, he is blamed for the corruption in the Banking Clan (especially when he was worried about his own legacy) and control of the Clan ends up falling to the Republic alone (giving Palpatine's future empire a large source of income for weapons such as the Death Star).
The trial of temptation in "Destiny". First, Yoda is given an apocalyptic scene of a hallway in the Jedi Temple with the bodies of fallen Jedi, including Mace Windu, Petro and Ahsoka Tano. To make the last even more heart-breaking, Ahsoka asks if she'll still be able to become one with the Force despite being cast out of the Order by the Council before dying. Then Katooni brings Yoda brings to a more idyllic scenario: there is no war, and everyone Yoda knows is still part of the Jedi Order, including characters who previously died (such as Qui-Gon Jinn, Tiplar, Knox and Adi Gallia) or left/betrayed the Order due to circumstances connected to the war (Dooku, Barriss Offee and Ahsoka Tano). Yoda really longs for those happier times, but he knows this isn't real.
The series finale Sacrifice. After seeing all the visions of Order 66 on Dagobah and the visions in Destiny, Yoda goes to Korriban/Moraband, confronts Ancient Dark Jedi and Sith spirits from variouseraspast and also Darth Bane himself before facing a final vision of him and Anakin facing Dooku and Sidious. They emerge victorious, but Yoda could not learn what was behind Sidious' veil as Palpatine detaches from the vision beforhand. At the end, Yoda is told that despite every suspecion the Council may have, the cannot prevent the future the best he could do is bring the teachings to a new generation as a Force Ghost and that Anakin will fall and the Sith will win over the Jedi. At the end there is a Hope Spot however—he sees that there is another Skywalker and perhaps sees the events of the Original trilogy leading up to the redemption of Anakin Skywalker and the fall of the Empire, along with his own Death. At the end, Yoda, having learned how to become a Force Ghost, infers to Obi-Wan and Mace Windu that while they may not win the war, by becoming One With the Force, a technique that the Sith can never master, they will be able to sow the seeds that will allow for victory over the Dark Side once and for all, showing that even in Darkness, there is hope.
Every time you watch an episode, keep in mind the events that we know are going to happened in the future: Anakin will become Darth Vader and Obi Wan, Padme, and Mace will all die by his hands, the Jedi will be mostly exterminated (meaning that every single Jedi character we see in the show will most likely be victims of Order 66), the 501st Legion will become Vader's personal hit squad, Yoda will be forced into exile for the rest of his life, Palpatine will turn the Republic in to an oppressive dictatorship, etc. This make all the 'happy' episodes (Every time Anakin and Padme reunite, the future 501st Legion soldiers in training, Yoda giving words of encouragement to the clones) much harder to watch.
On that note, there's the vision the Son gives Anakin of what he's going to become in "Ghosts of Moris." (Season 3, Episode 17) It's a rapid succession of scenes from the third movie, ending in an image of Darth Vader and the destruction of what is probably Alderaan. This is all bad enough, but then there's Anakin's reaction - he's horrified that this might possibly come true, and he's desperate to prevent it. This, combined with Dramatic Irony, just makes the whole thing even worse.
Real Life Example: One year prior to the airing of "The Lawless", Sidious/Palpatine's voice actor, Ian Abercrombie died, and the episode paid a tribute to him by saying "In Memory of Ian Abercrombie".