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Tear Jerker: Thomas the Tank Engine
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 lets him 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". 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".
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.
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.
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.
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 ending of "Dirty Work/Diesel's Devious Deed" where The Fat Controller sends Duck to Edward's station due to believing that he had made names for Gordon, Henry, and James. Duck lets out a tear on his eye, knowing that his friends and 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".
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.
"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.
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".