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Tear Jerker: Free!
In the first episode, before going into the abandoned swim club Nagisa states that "People have seen shadows moving around and hearing sobbing noises." In the next episode, we are treated to a short scene of Rin walking around in the aforementioned abandoned swim club, looking around with misty eyes.
The scene becomes much more heart wrenching once you've figured out that Rin is looking at a portrait of his deceased father with his swim team. The light novel reveals that Rin's father was once a swimmer with aspirations to become an Olympic athlete, but became a fisherman instead. He died in an accident while fishing - his boat sank and drowned the fisherman aboard.
Despite being overquoted, the "When you're ten, they call you a prodigy" line (quoted in full on the Memetic Mutation page, linked above) can really tug a heartstring, especially given the part that usually isn't included: "I can't wait til I'm ordinary."
Makoto telling Rei that backstroke is easier for people who are scared of water becomes one when you discover that Makoto is scared of water, as revealed in High Speed!
It is revealed in the second episode that Haruka and Rin raced, and the former easily won. Afterwards we see Rin crying on the floor and Haruka walking up to console him, only for him to pass him by, dropping his goggles.
"He went to a swimming school abroad, but it didn't make a difference."
"So that's why Haru quit swimming competitively. It's because he hurt Rin."
Rin telling Nitori about his father's dream to become an Olympic swimmer and how he died.
Rin visiting his father's grave before the tournament and asking his father to watch him.
Before he leaves, he gently fist-bumps the grave. It's sadder when you see it.
The look on Rin's face when he wakes up from his nightmare about his losses to Haruka and his father's death. He's sweating, breathing hard, and visibly shaken.
The ending of episode 7 Rin wins the race and tells Haru he'll never swim with him again. The look on Haru's face is heartbreaking.
In episode 9 when Rin ditches Nitori and leaves the festival to visit his old elementary school. He grips the fence hard as he imagines himself winning the relay with his team in elementary school, and remembers how much he loved being with them. Then he clutches his heart, stumbles, and runs away from the school, presumably in tears. The worst part? His exile from his friends is entirely self-inflicted and would be easily resolved if he would just stop torturing himself.
In episode 10, Haru recalls the first time he saw Rin after he came back from Australia. Haru was so happy to see Rin again, he actually was the one to run over to Rin and even smiled while openly talking about what was going on in his life. But Rin, acting strangely, challenges him to the aforementioned race, loses, and tries to run away. He's stopped by Haru, who asks him what's wrong, but Rin only says he's quitting swimming. It's clear that this has weighed down on Haru for a long time.
At the very end of episode 11, the look on poor Rin's face when Seijuurou told him that he's out of the relay.
In episode 12, when Rin lost his race by a mile and was so miserable he couldn't even find the strength to pull himself out of the pool. He struggled trying to pull himself out, but kept slipping. It hurt to watch. Haru saw something was seriously wrong and ran out of his seat to see what was the matter with him.
Haru's emotional breakdown when he hears Rin is quitting again. He's really not going to be able to swim with him again this time. He's so overcome that he slides down to the ground and buries his head in his arms.
When it's revealed that Rin got the crap kicked out of his self-confidence in Australia and when he lost to Haru. He acts confident, but actually has very low self-esteem because of what happened. The bigger tearjerker is when this comes to a head in episode 12. Rin rages over being kicked off the relay and losing his race so badly, kicking things around and yelling at Nitori, and storms off swearing to never swim again. Then there's his whole speech when Haru finds him.
Rin: Haru...Why are you here? Come to laugh at my pathetic loss? You saw what happened in the free. And I was taken out of the relay. The world is laughing at me. So join in! No need to pity me. (Haru is silent) I told you to laugh! That's all I'm good for, anyway! I'm not even good enough to race you guys in a relay.
And when Haruka tries to calm him down, Rin gets angrier and charges at Haru, grabs him by the jacket, yells in his face, and tries to punch him. They end up struggling on the ground, with the music getting faster and more intense...until Rin sees that Haru wrote "For the team" by the sakura tree, and (as mentioned above) realizes Haruka remembered that, and was thinking of him.
After that, Rin actually breaks down crying, asking Haruka "Why? Why can't I be free? I want to swim with you guys. I want to swim in a relay with you guys. But it's too late now."
It's worse than that. Rin doesn't ask "Why can't I be free?", he asks "Why isn't it 'Free'?", because "Free" was what Haru wrote on his brick and Rin was the one who wrote "For the Team". This is translated incorrectly by several subbers.
Season 2 (Eternal Summer)
How about the OP? Nagisa crouched near the wall like he's about to cry, Haru getting unnaturallypissed, Haru crying, the prospect of most of the swim team we've come to know and love graduating... it's preparing us for the oncoming heartbreak.
Episode 5. It's foreshadowed that because half of the main characters are graduating and have been filling out surveys for their career prospects that inevitably there'll be a character crack under the pressure. However, this happens to Nagisa of all people. It's disheartening enough seeing the one member of the Iwatobi swim team who's always smiling look so unhappy, but it's worse when we learn how miserable he is at the prospect of quitting the swim team. Especially since the fear of giving up something you love in order to "succeed" in life or satisfy a social standard is something a lot of high schoolers (and college students) could relate to.
In episode 9, it's Haruka who cracks, in a big way. He straight-up stops in the middle of a race.
Watch the animation while he's swimming. In his close-ups, the water darkens around him, the same way it does around Sousuke when he swims. It's likely symbolic of how the stress of having to give up swimming "free" is making swimming as painful for Haru as it is for the physically injured Sousuke.
Episode 9 ends with Sousuke sitting underneath a shower, clutching at his shoulder and groaning in pain.
This troper would also like to mention that he was all alone while that was happening, and based on how it just ended on that note, he stayed like that until he could get up, despite the searing pain he was already feeling.
Also, look at the close-up on his shoulder. It's reddened and sore-looking. His injury is getting worse.
Again from episode 9, Haru losing it and yelling at Rin when he comes to ask what happened during the race. This is Haru, who never raises his voice or loses his cool. Seeing him snap is just...jarring.
Rin: Do you not understand that what you do out there is going to impact your future? Don't you have a dream?! Take this more seriously! I know you could -
Haru:(slams his fist against the lockers) You're the one who doesn't understand! What dream? What future? It's you who cares about all that! I'm not you! I don't have any of that!
Even worse is the completely stunned looks on the other boys. Rin in particular looks like he got slapped in the face.
The wording adds a whole other level of heart-wrenching. Haruka literally says that he doesn't have a future.
And then there's Episode 10 in which Sousuke tells Rin that he has entirely given up on his dream.
After he realized that his shoulder injury could end his career in swimming, he keeps working it harder in physical therapy, but it was already too late and nothing could heal it. By then, he could only watch as his teammates surpassed him (a former champion), when his chances of ever improving were gone for good.
Sousuke: My impatience grew...And then one day I realized. My dream was never going to come true.
As Sousuke tells his story, Rin is increasingly horrified and upset, and ends up driven to tears.
The worst part is that this could have been completely avoided if Sousuke wasn't so driven. He noticed early on that something was wrong with his shoulder, but instead of stopping training to address the problem, he ignored it and kept working himself harder and harder until he'd completely wrecked his shoulder. His passion for swimming ended up making him unable to ever do exactly what he loves most.
Haru and Makoto's argument in Episode 11, in which Makoto confronts Haru about his future plans and eventually reveals that he's going to a university in Tokyo. What really drives it home is how hurt Haru is about Makoto finally calling him out on avoiding talking about the future and how the latter is leaving him behind.
Makoto: I meant to tell you sooner, but I just couldn't find a way to say it. I...
Haru: Do whatever you want!! (Runs off)
They're also both close to tears throughout the whole argument, and Haru is shown curled up in a fetal position beneath his duvet the next morning, his clothes strewn across the floor. It looks as if he's cried himself to sleep.
And when Haru, in a fit of emotion, yells at Makoto that all he ever does is meddle with everyone and to stay out of everyone's business. Although he most likely didn't really mean it and only said so out of frustration and impulsiveness, Makoto's hurt expression◊ is heartbreaking. What makes things even worst is if you've read High Speed; Haru constantly thinks to himself of how Makoto always meddles into situations. Whether it being to troublesome or not wanting to hurt Makoto's feelings, he never goes out of his way to actually say it, until now.
All Makoto has done for nearly two whole seasons is try to help his friends and put everyone else's needs before his own, and now the one time he does something for himself, his best friend throws it back in his face as an insult. Ouch.
In episode 12 there's a flashback to when Rin started going to school in Australia, and how he had trouble fitting in at first. He tries to win his class over by giving his "I have a girly name, but I'm a boy" speech, but due to the cultural barrier the class just looks confused. Later, when he tries to tell his classmates about cherry blossoms, none of them seem to understand that either. We then cut to Rin walking alone, looking dejected.