A/N The Sodor Tales and Thomas Tales are in a timeline all their own, but both Sodor and Thomas Tales are in that timeline. For those who read Sodor Tales, this occurs before Edward's End Of Line, one of the Sodor Tales.
One day, Thomas was pulling Annie and Clarabel, but things went wrong in Knapford. Emily was in Knapford as well and she was a runaway. Runaway Emily hit Clarabel and the accident left Emily, Annie and Clarabel fatally damaged.
Thomas was told of Emily, Annie and Clarabel's outcome by his driver and he burst into wailing sobs, big tears coming out of his eyes without stopping, devastated by the loss of the Steam Team's big sister figure and his faithful coaches. His driver pressed a cloth to his eyes, doing what he could to comfort his tank engine.
"There, there Thomas," his driver said soothingly. "You couldn't do anything and I couldn't either. There was no time. Just go ahead and cry. I shall be here to dry your eyes."
Thomas sniffled, sobbing too hard to speak. He cried more, allowing his driver to keep drying his teary eyes. First my siblings, then my love Ashima, now Emily, Annie and Clarabel, he thought. All gone to The Big Railway In The Sky. I've lost human friends, too. My old crew, in some cases, The Thin Clergyman and my friends from the line, some, like Janie and her brother have gone to their reward.
His driver said, as he continued to wipe the tears away, "When you cry in my presence over what's just happened, I'll let you have my comfort. Cry as much as you want and I shall dry your tears. I want to be supportive and understanding in this time. You've got a right to cry and I plan to give you compassion when you do". He gently wiped his engine's eyes.
After a while, Thomas's sobs subsided and his tears slowed to a stop. His driver softly dried his last tears, rubbing his cheeks and wiping his damp eyes dry.
Thomas said, "Driver, you genuinely touched my heart with your care for me in this time, now and when I cry again."
Thomas's driver replied to his engine, "I know you feel things deeply, though you tend to be a happy little engine when circumstances permit. You're a sensitive soul, so caring and compassion are what I feel you need.", then called Sir Topham Hatt on the telephone to tell him about Emily, Annie and Clarabel.
Thomas gave his driver a soft look to say "I appreciate your love and comfort.".
Thomas's driver said, "There's to be a meeting here later, when the other engines that are working finish their current jobs."
Thomas had a drink while waiting for the other engines to come.
The other engines came to Knapford for the meeting. They were told about the loss of Emily, Annie and Clarabel. Thomas, barely able to choke out the words, gave a speech about the fallen through sobs. His driver held a cloth to his eyes.
Thomas sniffled and began in a broken voice, "I lost my faithful coaches and, Steam Team, we lost our big sister figure. We shall miss Emily and I'm devastated by the loss of my coaches. It's fine for us to be dreadfully sad they've gone to The Big Railway In The Sky, but we must carry on and be Really Useful Engines. At least after we have a memorial service for our friend, Emily, if we can. I want Annie and Clarabel to be memorialized as well. Maybe a part at the beginning just for my branch line for them and then a part for Emily.". He had nothing left to say after that, except what could be said with his constant tears.
Thomas pressed his buffers against Edward's, Henry and Gordon did the same with each other, Percy and Toby, James and Duck, as Duck thought it was only fair James have someone hug him, along with Nia and Rebecca. Their drivers comforted the sad engines, too. All the engines that were on the Steam Team at some point had a friend to press buffers with in an engine hug as they cried together, Thomas, Edward, Henry, Gordon, James, Percy, Toby, Nia and Rebecca, especially the Ffarquahar engines, were weeping. Percy especially viewed Emily as a big sister figure and was wailing his broken heart out over her death. Thomas, like his best friend, though not quite as much, viewed Emily as a big sister figure, so that combined with losing his coaches, was why he was wailing with grief, too, just as his best friend was. They cried and cried and cried, the tears and wails not stopping until they had no more tears to cry. Duck was just there for his friend, even though he was never on the Steam Team, passed over in favor of Emily.
The railway was closed for a while to allow Emily's friend grieve and for the memorial service for Emily, Annie and Clarabel Thomas wanted. The more emotional engines, like Thomas, Edward, Henry, Percy, Nia and Rebecca cried their eyes out, Toby and even Gordon and James sniffed, with Toby the most weepy of that trio because he was more emotional that the others and was a Ffarquhar engine for a time. Thomas and Percy had the most tears, as they were the closest to Annie and Clarabel of all the engines, and Percy's strong feeling of Emily being his big sister figure. During the days following the memorial service, the engines often cried together or in Toby's case, with Henrietta. Henry would usually visit Thomas or Edward if he needed to cry over Emily, as they were more understanding than Gordon and James, who would 'probably call me a big cry-enigne', Henry thought. Percy, if he felt weepy and wanted a friend to share his tears with, would cry with Thomas because they were best friends. Thomas's driver gave the tank engine care and compassion when present for his crying spells. He let his engine vent, validated his emotions and softly dried the tears from his eyes. Thomas shed a great many tears, whether with engine, human or a mix of engine and human friends, completely open when he had to cry. The engines had each other, their crew, the Hatts and any other human friends who happened to be around for comfort, even when the railway reopened, as the more emotional engines were still in grief then, though they could work. They might do a job, then cry and sob after it was done. But in time, even they recovered as much as they could. Molly replaced Emily on the Steam Team and another engine took her old work over. Replacement coaches for Annie and Clarabel were obtained for Thomas's branch line and the railway work took on a more normal flow again, the NWR's new normal after the loss of Emily, Annie and Clarabel.
A/N James and Duck are said to be affiliated with each on the wiki and I read somewhere Duck was considered for the Steam Team, but replaced on it with Emily ultimately. Molly replacing Emily came from somebody saying if they wanted more female characters, they could've put her on the Steam Team instead of creating Nia and Rebecca.