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- "The Sad Story of Henry/Come Out, Henry!" is this in spades. As a result of refusing to leave the tunnel, Henry is bricked up by the Fat Controller "for always and always and always" (although in the US Version, It was only "until you're ready to come out!"). By then, he becomes sad and miserable that no one would ever see his paint again and and that he is never being allowed to journey out again. The publishers of the original novel found the ending so downbeat they only sold Awdry's work so long as he created a happy ending via "Edward, Gordon and Henry/Henry to the Rescue".
- In the Shining Time Station episode: "Does it bite?", Mr. Conductor did not blow his whistle to begin the story because he was too choked up about Henry and his punishment. As he blurts out to the kids in tears, "But I must warn you! It's a very sad story!"
- The atmosphere and music is perfectly-executed. After the tunnel is sealed, it goes all quiet, birds are chirping, trains pass-by, Henry is unsure of himself. Then the background theme goes very sad as Henry realizes what a fool he's been, he's all alone, and its too late to set things right.
- Speaking of next episode, there's the scene where Henry laments on his misbehavior and wondered if the Fat Controller could ever forgive him and let him out of the tunnel.
- In "Thomas' Train/A Big Day For Thomas", Thomas had nearly cried after realizing he wasn't coupled to the Express. As soon as he returns to the big station, everyone was talking angrily about the incident just until they noticed how sorry Thomas was.
- The beginning of "Troublesome Trucks/Foolish Freight Cars" where James (as pictured above) remorsefully cries about all of the trouble he's caused with the coaches, particularly mending a hole in one of them with a passenger's bootlace. The tears from his eyes definitely show how terribly sorry he was for his actions.
- One scene of "Thomas and the Guard/Thomas and the Conductor" has Henry moaning of his poor condition to Thomas, who was very dismissive of the issue, bluntly telling him that he's "too fat/slow and he needs exercise". You have to feel for Henry for his current condition.
- From "Thomas, Terence, and the Snow/Terrence the Tractor", Thomas gets himself stuck on the snow and then realizes how silly that he was for breaking his snowplough just right before he begins to cry.
- After constant failings, the Fat Controller sadly informs Henry that he'll have to send him away if his health doesn't improve in "Coal/Henry's Special Coal". Both Henry and his driver seem pretty choked up by that, and even the Fat Controller seems to take every action to avoid it happening. Thankfully his Welsh Coal is brought into the situation.
- In "Toby and the Stout Gentleman/Toby the Tram Engine", the passengers wish Toby one last goodbye after his controller decided to close the line, leaving Toby in the shed lonely and unwanted. That is until his driver wakes him up for good news: an important letter of a certain stout gentleman.
- In "Thomas In Trouble", there's Thomas sadly leaving the line after the new policeman brands him a "regular law breaker".
- In "Thomas and Trevor/A New Friend for Thomas", Trevor lets out a tear due to the fact the day's work at the harbor was over.
- The ending of "Dirty Work/Diesel's Devious Deed" where The Fat Controller sends Duck to Edward's station after accusations he had made names for Gordon, Henry, and James. Duck lets out a tear on his eye, knowing that his friends and (seemingly) even The Fat Controller are against him just as Diesel, who had made those names in the first place, watches him with a sinister grin on his face.
- Henry feeling devastated when a forest was decimated by a storm in "Henry's Forest". Toby feels very bad for him, explaining to Sir Topham Hatt that the forest was a special place for Henry.
- The ending theme of "All At Sea" as the narrator said "Duck still wonders about the lands beyond the horizon, but he enjoys being with friends most of all and I think he knows that sometimes the best travels are those we can only dream about. Don't you?"
- The latter half of "Granpuff" when Duke is left behind and Falcon and Stuart head off to their new home. Think of it as someone being separated from his own children. Now that, is a real heartbreak.
- Mrs. Kyndley tearing up in "Make Someone Happy" when her daughter wasn't able to visit her.
- Salty's pining for the sea in "Salty's Secret".
- In "Thomas and the Birthday Picnic", there's Thomas becoming sad after failing to find a perfect place for Dowager Hatt's birthday picnic. It's even sadder when he realizes that he ran out of ideas, thus upsetting the Hatt Family, complete with letting off a low sad whistle.
- In "Thomas and the Statue", there is the scene where Thomas sadly clears the snow with the snowplough after realizing that his boasting about him being on the statue had alienated his friends.
- "Toby's New Shed" has Thomas eagerly attempting to do a charitable deed for Toby by helping make a new roof for his shed, only to be confused when Toby doesn't seem too keen on the idea. When the job is done and Toby is downbeat, he doesn't understand and asks what's wrong. Toby somberly explains he liked having his old leaky roof, as birds were able to come in and take shelter, his home was their's, and a guilt ridden Thomas watches as rolls sadly into his new shed alone. Luckily Thomas fixes this by arranging a bird house to made right next to his shed.
- There's a moment in "Thomas and the Rainbow" where Thomas, after obsessing over finding the end of a rainbow and thus neglecting his friends, becomes derailed. Seeing Percy on another line, he shouts and whistles for help, but Percy puffs on, seemingly taking no notice and leaving Thomas behind. Thomas sadly remembers that, because he was rushing to find the rainbow's end, he brushed Percy aside when he wanted to talk earlier. Because of his silly obsession, Thomas has lost his best pal and is stranded without hope.
- But this is not the case. The rest of the episode turns into one long heartwarming moment, as we learn that Percy, in fact, did hear Thomas' whistle, and was puffing on because he was in a hurry to get help! The message is passed from Percy to Harvey via a large number of other characters, all of whom are anxious to help their friend. Even more heartwarming because the helping characters include several others whom Thomas had spurned earlier.
- In "Duck and the Slip Coaches", there's Duck left alone in the sheds very sad because James had stolen his idea of bringing in the slip coaches for the passengers.
Duck: "But I told James about the slip coaches. It was...my idea."
- It's no secret to the fandom that Emily is quite a Base-Breaking Character. However, when she came back to the sheds and found them completely full (as Duck was sleeping there for the time being), one can't help but feel sorry for her. And if that isn't enough, the next night, Duck is there again, and Henry takes up the last berth, leaving Emily outside again. Worst of all, no one else pays her any mind at all! Honestly, this was just taking the "Emily replaced Duck!" spiel too far.
- In "No Steam Without Coal", there's Timothy left upset over Bill and Ben's remarks about him being no fun and is the odd one out, making some feel that the twins' teasing were taken too far.
- Thomas' increasing jealousy towards Stanley in The Great Discovery as he starts feeling left out, especially during his Jerkass Realization after trying to play a trick on him only causes an accident and leaves him shunned.
- The Fat Controller receiving the telephone call that Thomas has been lost at sea in Misty Island Rescue.
- Percy's growing worry as chances of Thomas being found diminishes. When he does find Thomas their reunion is a Crowning Moment of Heartwarming.
- Luke and Victor's backstories in Blue Mountain Mystery. GOOD GOD.
- Stephen trying to find his special job in King Of The Railway. Being a refined version of one of the first engine designs built, he spent most of his early life as The Ace, however in the modern world, Stephen is slow, outdated and unable to pull even small loads current steam engines can. He is rejected every place he tries to prove his worth (despite sympathetic treatment from Paxton and Skarloey) and finds his old mines to have closed down, lamenting sadly he now has no place on the railway.
- Tale of the Brave:
- Right after the Scrap Heap Monster incident. It ends with Percy completely rejecting Thomas AND James.
- On the same coin, Thomas still wants to make amends, but it doesn't go well at all.
- While they're looking for him, Thomas thinks that Percy is leaving Sodor forever on Gator's boat. After the initial moment of horror, he rushes to the docks, only to find the boat is already leaving. He whistles and screams for the boat to stop, but they don't hear him. As a last ditch effort, he gets Cranky to snag the boat with his hook, but the crane nearly falls off the docks while pulling the ship back to the port.
- Gator's goodbye. Seriously, Percy looks/sounds so sad through the whole thing, as opposed to Hiro's departure.
- Right after the Scrap Heap Monster incident. It ends with Percy completely rejecting Thomas AND James.
- Sodor's Legend of the Lost Treasure:
- Most of the scenes involving Thomas and the Fat Controller (whether directly or indirectly) feel this way, especially because this is the strictest he's acted in years. The worst one of all, though, is after the dynamite scene, where the Fat Controller shouts at Thomas and sends him away, not having seen enough to know that Thomas was simply trying to save everyone from getting destroyed. It's a gut punch at its finest, because more often than not, his harsh words towards Thomas are mostly justified. His behavior towards Thomas also feels much more strict than towards the other engines this time around, which makes things feel worse still.
- Sailor John indirectly accusing Thomas of taking the treasure. Thomas' expression as the sailor rolls away in Skiff really seals it.
- The worst part is that Sailor John and Skiff usually appeared not long after something happened to dishearten Thomas, and his mood improved quite a bit whenever he met with them. But now even that was taken from him...
- The Great Race:
- The scene where Sir Topham Hatt tells Thomas he can't take part in the Shunting Challenge due to his accident, and that Percy has to take his place. Sir Topham looks legitimately heartbroken during this scene, like a parent telling his ill child that he can't come on vacation with the rest of the family. It doesn't help that Percy is worried about competing, and Ashima coming in to say goodbye before they all leave for the Mainland. The scene ends with Thomas alone at the Steamworks looking miserable and heartbroken.
- "The Island Song" could make some nostalgic and long-time fans tear up.