Thomas the Tank Engine/WMG

The Fat Controller's railway is in deep financial trouble.
This is why characters like Boco have disappeared-unable to keep afloat, Hatt has been selling some of the more expensive engines off to other railways. This is also why certain new characters "arrive on the island" or are "on trial" but are never seen or heard from again- they were on loan to the Sodor railway and their own managers take them back after a few weeks. The Fat Controller can only afford to buy and keep extremely outdated models, such as Emily. The Fat Controller hasn't told the engines yet as he wishes to keep their morale up and have them working at peak efficiency.
 * This could explain why he's rarely in a good mood.

The series is a fantasy of The Fat Controller, who is locked in a mental asylum and is imagining the adventures all in his head.
As shown in this Webcomic.

The Fat Controller is a Highlander Immortal.
He was a director of the railway when it was nationalised in 1948. He's still around, not a day older, sixty years later. The Other Wiki says the office of Fat Controller is hereditary and the present one is the original's grandson, but that's just a cover story.

The Fat Controller is a wizard.
This is why (in earlier seasons) he's able to seemingly appear everywhere; he apparates.

The Fat Controller is a robot.
This would also explain why he's been around for a long time. Someone installed a robotic version of him so he could keep the railway going after his death.
 * This is also why he can have talks with the trains.

Thomas is a lost vehicle of James Bond.
This explains how he's able to fly over the canyon without trouble and how he crashes through stuff but avoids getting scratched. Thomas was meant for the secret service, but he got loaned out by The Fat Controller's railway (it was meant to be a loan). The railway ended up "losing" him. (Thomas's crew just settled down, and he ended up being written off as "lost".)

The engines are all Transformers in Mode Lock
Probably old ones, hence the outdated designs.
 * You mean this?

Sir Topham Hatt is Mavarah
To bring the mode locked Transformers theory and the spheus magna= cyberton theory at Bionicle full circle, maybe Sir Topham Hatt is a fully oranic Mavarah.

The Island of Sodor keeps steam trains around as tourist attractions.
The Island seems to be too small for such a varied a train network to be very useful, and there's no reason to keep them around when diesel and electric engines are available. Clearly the old-school trains are a big tourist draw. The engines themselves are either in denial or don't like to bring it up, and it would explain why diesel engines look down on them. The TV series of course pays no attention to real railways anymore.
 * The network isn't that expansive, at least not in the Railway Series - the standard gauge lines only cover about half the island (if the populated one), and consists of a single mainline with half a dozen branches - but still enough to keep at least 80 locomotives in work, according to background material. Diesels are used, and one of the branches was electrified from the start, but alongside steam instead of replacing it. The engines are still doing real work, but tourism probably does matter though - the books exist in the Railway Series universe, and made the engines famous long before they were ever at risk. The Narrow Gauge lines are tourist attractions (being based on real ones), although two of them do transport goods, and were built for that purpose.

Thomas takes place in the same universe as Questionable Content.
The trains run off standard AnthroPC AI, which is prone to all kinds of personality quirks and conflicts; the continued presence of steam power is because locomotives evolved differently in this verse than ours. Sentient steam locomotives don't show up in QC, either because passenger trains are even less a part of the transportation system in the US than they are in Real Life, or because Sodor is an experimental test bed for them.
 * Or both.

The Fat Controller is Oskar Schindler for sentient steam trains.
Zealous plans to modernise the rail network involved scrapping all the steam engines, and the Fat Controller bought as many as he could to save them. Dr. Beeching's Final Solution?

In robot mode, Thomas has a Kanohi Olimak and a shield with 50 Rhotuka Spinners
See Sir Topham Hatt is Mavarah and The engines are Transformers.

Donald and Douglas also have Beast forms downloaded from The Bahrag
Just for fun. Both of them are Twins.

The trains are all suicidal.
Having almost no control over their own lives, they are trying to end it all. Why else would they get in all those crashes? They're trying to make it look like an accident because they don't want to traumatize any kids who might be watching. The Troublesome Trucks don't even hide the fact that they want to die. In fact, they have managed to smash themselves to bits. The steam engines are still trying.

The Great Time War has messed with the history of Sodor.
This is why, in "Hero Of The Rails,". This also explains why Negative Continuity starts to come into play from season 6 on and why characters such as Elizabeth The Vintage Lorry and Fearless Freddy exist without any regard for Railway Series continuity. The Great Time War blew out whatever connections the television series reality had with its source material and altered the history of Sodor.


 * alternately The fifth Blackadder's trip through time messed with the history of sodor

"The Magic Railroad" as seen in The Movie is not the only Magic Railroad.
Rather, it has numerous branchlines that connect to other worlds, and these also have engines which travel back and forth on them.

The Island of Sodor is in the same reality as Stephen King's "Trucks".
The trains eventually took over, forcing the humans to build tracks everywhere, which is why they're able to go pretty much anywhere they please. The "conductors" are merely humans who sit in their control boxes, pulling levers that do nothing as the trains guide themselves to make the humans think they're in control somehow. Sir Topham Hatt is just a puppet who kissed up to his locomotive overlords, and thus they make him perform acts that suggest he is in charge, when really the trains themselves are. That's why trains that are "sent packing" come back so soon- he has no real authority in Sodor. As for non-trains, such as George the Steamroller, Terrence the Tractor, and Bulgy the Bus: they're plotting to take over Sodor and rule over the humans, as evidenced by their hostility towards the trains (Bulgy's anti-railroad sticker should be enough proof).

Sir Topham Hatt is jinxed.
Every bad that that happened in Sir Topham Hatt's presence is a direct result of him simply having been near by. This is because he is haunted by the spirits of the Coffee Pots, four engines Word of God states were built by Hatt as a young engineer which were later scrapped.

Sodor Island has been hit by a mass retardation.
The train drivers and engineers of Sodor are constantly getting into accidents that could have been easily prevented. Broken rails, roads, bridges, and tunnels are almost never repaired. Several signal stations and unsafe areas (like the quarry with the huge boulder that almost destroyed six engines) are left unattended or plain ignored. The sentient trains suffer under the control of their well-intentioned but unskilled drivers.

Sir Topham Hatt is the only level-headed man around; unfortunately, he is Surrounded by Idiots. He blames the mistakes on the engines so the people don't have to come to terms with their own incompetence.

The Sodor Island Railway was the inspiration for the EVA Project.
Yes, another one of those!

After his beloved railfan son was hit and killed by one of his trains, Sir Topham Hatt (a lifelong spiritualist) wondered if his soul may have clung to the blue tank engine that killed him. British Rail wondered if sentient locomotives, able to actually hear orders for themselves, might make train service more efficient. With assistance from Aleister Crowley and biomechanics developed in undisclosed experiments by distinguished Ger-umm...French scientists, the "Living Train" was a success. However, due to the psychological trauma of engineers melding their souls with the locomotives (as well as the locomotives' occasional unwillingness to blindly follow 'all' orders), and a number of mysterious deaths of railway personnel, the British government immediately ended the experiment and ordered the engines scrapped.

About half a century later, Japanese robotics professor Gendo Ikari chanced upon a story of the "Sodor experiment" in a journal...


 * So... Choo what thou wilt?

Thomas' character arc is a Deconstruction > Reconstruction of I Just Want to Be Special.
Thomas the Tank Engine is one of the most well thought out and complex protagonists in a children's series.

Starting off as a meek, excitable, and childish engine, he loved playing jokes on the engines, but he wasn't particularly well liked by them, except Edward, who could be said to be a big brother figure to him. It became obvious that his constant jokes were cries for attention, as he was tired of shunting in the yard and wanted to explore the world. He wasn't happy with the mundane, he wanted to be special. However, the first few tastes he had of the "real world" were not pleasant (tricked into running with Gordon's train, forgetting his coaches, being pushed by freight cars). Despite this, he was determined as ever to go out on his own. Recognizing this, he was given his own branch line as a reward for saving James.

However, he clearly overestimated himself. He'd leave his conductor behind, beat up his snowplow because it was uncomfortable, and in general was a kid being given a big shiny toy. Despite this, he was convinced he was the most important part of the railway. He eventually meets Percy, who takes his old job as the shunter in the yard. The two become fast friends and Thomas acts as a mentor to him as well, however questionable of an influence he may be. Even though he was running a branch line, he was still irresponsible and goofy, teasing Gordon about falling into a ditch until he ran into a mine. Despite this, he would still tease Percy, fancying himself to be above him. The two bickered a lot, from coal to ghosts to wooly bears, possibly stunting Thomas' growth. For most of the second season Thomas is out of focus, though what we do see of him he seems rather arrogant until he has his accident with the stationmaster's house.

It's obvious to tell from here that he has what could be considered a heroic BSOD. He isn't the invincible engine he cracked himself up to be, and to add insult to injury, he's temporarily replaced with a diesel. The idea of the steam engines being replaced hangs over them for much of the series, and even temporarily, it took a toll on Thomas' psyche. He comes back a wiser, smarter engine, and after one more childish quarrel between him and Percy, he matures into a role model to the little green engine.

By season 3 he takes an extremely different tone. While he does make occasional quips, he mentors Percy much like Edward did the same to him and almost always works with a smile on his face. We see his anxiousness of being replaced again reappear in Thomas Gets Bumped, where he puts his job on the line to get some children home. However, the Fat Controller recognizes his big heart, and lets him off for it. Similarly, whereas he used to think himself as the best, he clearly takes offense when James insists the same, and says "we're all useful, the Fat Controller says so, and he's the head of the whole railway." None of this is any more prominent than Trust Thomas, where he works his hardest to make all of his friends happy, and even when he gets hurt, he still wears a big smile on his face. His replacement complex is evident in Thomas And Stepney, where Thomas is jealous of the attention Stepney gets, along with the fact that he was shunted to let him pass. Despite this, Thomas is a sympathetic individual and the two become good friends.

Thomas begins the series with most everybody looking down on him, and through steam, coal and tears, becomes one of the most respectable and admirable characters on the whole railway, who pours his heart and soul to make sure he does a good job and everyone is happy. While the series deconstructs the troubles that come along with wanting to be "special" it also shows that it is also possible to overcome these troubles.

tl;dr: Thomas starts off a brat, wants to be special, realizes being special is hard, and grows up.

...and let's forget anything after season 4 happened.

Whiff is an Almighty Janitor
Whiff originally pulled the Mechanical Engineer's saloon coach on the mainland, which was a high profile job. After an accident that damaged and blinded Whiff greatly, a replacement was built, which meant the damaged Whiff was to be scrapped. Unknown to everyone, Sir Topham Hatt sent a team of workers to steal the damaged Whiff before he was to be cut up (ala Oliver) and sent him to the Steamworks. Everyone on the mainland now thought that the new Aerolite was the only one of its kind with the original destroyed. Sir Topham Hatt spent much time mending him, and eventually put him back in service. Whiff had forgotton about his previous life due to the amount of repairing they did. Not wanting to attract too much attention because he was the original and also to avoid being arrested for stealing the engine, Sir Topham asigned him to work in the waste disposal yard and gave him glasses to help his sight. However, sub-consciously, Whiff carries greater skills other than shunting. Also explains why he knows alot about of Sodor history, having spent his time at the Works hearing the tales of the railway.

'Thomas and His Friends' will be the last book in the Railway Series, and will answer all unanswered questions.
Why? Quite simple. It is book number 42. The answer to the Ultimate Question of Life, The Univere and Everything.

The TV Series, at least at present, is actually about a boy's train set
That's why there's no regard for real railway operations - the kid doesn't know any better, and just does what looks cool. The engines being alive, and all human characters, are his imagination. The Steamworks is his dad's workbench, where all the damaged models are repaired (Victor and Kevin representing father and son). Thomas has such a heavy focus because it's the boy's favourite, so he uses it and features it in his stories more than any of the others.