Once they turned the bathroom into his actual office, basically it was a case of taking a silly joke alittle too far.
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Well the OP's question still stands: "What on earth were they thinking?". It may have been a running joke in the beginning but to actually turn the restroom into an office with a desk was just plain idiotic and not very funny.

I often wonder if people read through ALL the replies before posting.
Looks like this guy didn't before repeating.
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Exactly! He said it twice already.

You already asked this earlier and someone replied.
Did you miss that?
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I think though that I might saw a scene with Fonzie sitting at a desk in the bathroom and he says come in my office or something like that. It's when Happy Days got very surreal around the 5th or 6th season.

They should've added on fart sounds and sounds of urinating whenever Fonzie and someone else stepped into his office. It would've given it some gritty realism.
AiTF would put in a toilet flush for a gag.
Did we ever even once hear the toilet flush on HD?
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Or right after he dumped a really big one.
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Imagine if The Fonz would have given his signature "Aye!" every time someone flushed the toilet in his office!

LOL! It would have made it more realistic.

They should've added on fart sounds and sounds of urinating whenever Fonzie and someone else stepped into his office. It would've given it some gritty realism.

OK
So that explains it.
The Fonz has a weird bodily function fetish.
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The Fonz used the restroom for an office because he liked the smell of urine and excrement.

Hope there was an exhaust fan in there!
Exactly.
Smelly turds do not belong in an office.
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Hope there was an exhaust fan in there!

Yeah well that was dumb too, another stupid post-shark plot

He's not random you dolt. He owns the place.

What on earth were they thinking?
It was a running joke, since Fonzie called the mens' room his office from almost the beginning. To me it indicates his male chauvinism. Women are not to be involved in decision making!
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After Chachi burned Arnold's down they rebuilt it and for some idiotic reason put a desk and private phone in the men's bathroom so Fonzie could conduct business (??) in there - can you imagine going into a public restroom to pee and seeing a random leather-clad man sitting behind a desk? What on earth were they thinking?

Was there an episode where they had Fonzie sitting at a desk in the bathroom? I swear I saw that.