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Tear Jerker: Thomas the Tank Engine
"Oh dear. I'll have to stay here for always, and no one will ever see my lovely red paint ever again."
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In "Thomas and Gordon/Thomas Gets Tricked", while Gordon drags Thomas along with his Express train to pay him out for teasing him, Thomas sadly cries out that he will never be the same engine again and his wheels will be quite worn out.
The start of "Edward and Gordon/Edward Helps Out" shows how the other engines mistreat Edward for being old and will never be let out to journey again. Just until his driver asks if he's ready to be let out of the sheds, feeling happy for the first time in years.
"The Sad Story of Henry/Come Out, Henry!" is this in spades. As a result for refusing to leave the tunnel, Henry is bricked up by the Fat Controller "for always and always and always" (In the US Version, It was "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 busy sobbing about Henry and his punishment. As he blurt 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 realises 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 remorsefully cries for 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 can easily show the audience that he truly is sorry for upsetting the Fat Controller.
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". Even if Henry isn't seemingly that ill, you can't help but to feel sorry for him after that.
From "Thomas, Terrence, 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.
At the start of "Tenders and Turntables", the narration implies that Gordon and Henry have missed Thomas after he left the yard to take charge of his branch line.
In the last scene of "Trouble in the Shed", Gordon, Henry, and James, who were sent to the sheds by the Fat Controller, were feeling remorseful for their behavior by going on a strike.
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.
The beginning of "Whistles and Sneezes" has Gordon expressing his jealousy towards Henry and his irritation of him returning from crewe with a new shape and is happier than he's ever been. This left Henry feeling noticeably hurt of Gordon's remarks.
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".
The final scene of "Off The Rails/Gordon Takes A Dip" shows Gordon in disgrace after falling into a ditch due to his stubborn refusal to pull trucks, which he deeply regrets.
From "Down the Mine", there is scene where Thomas lets out tears after realizing how foolish it was for him to pass the danger board and fall down a mine while he was being lectured by The Fat Controller.
In "Thomas and Trevor/A New Friend for Thomas", Trevor lets out a tear due to the fact the days work at the harbor was over.
The latter of "Percy Takes the Plunge" where Percy is fetched out the water, cold and miserable, and is then pulled away by an amused Henry on his goods train.
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.
Thomas in disgrace after crashing into the stationmaster's house in "Thomas Comes to Breakfast", after a cleaner accidentally fiddled with his controls.
Henry feeling devastated when a forest was decimated by a storm in "Henry's Forest". Toby feels very bad for him, explaining that the forest was a special place for him.
There's Mrs. Kindley sobbing due to her sister being unable to visit her in "Make Someone Happy".
Salty's pining for the sea in "Salty's Secret".
Emily feeling sorry for Thomas after The Fat Controller reprimands him for not having his snowplough fitted in "Thomas, Emily, and the Snowplough". This is intriguing considering that Emily had a domineering attitude towards the blue tank engine earlier.
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.
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 Breaker. 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.
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.
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.