According to a review in the Wall Street Journal: The fly has become a symbol of the loss of control in Walt’s life, so its defeat is all that’s important to him right now.
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I think it's about little things escalating to big things.
The episode starts with Walt noticing .14% of each batch coming up short.
He's detected Jesse's skimming but doesn't know it yet.
The fly represents nagging doubt.
A little minor annoying thing, which leads to a bigger thing (losing his shoe) which leads to a bigger thing (falling off the mezzanine).
What problem, little today, if neglected will escalates?
A downfall starts tiny.
Walt has his secret betrayal too, about Jane's death, which he almost discloses after Jesse drugs his coffee with sleeping pills.
One more candidate for Walt's undoing.
By the way, this is what is known as a "bottle" episode .
Small setting, small cast, small budget.
Like a fly in a bottle.
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I think the meaning of the fly was that Walt's cancer came back.
On the same episode, Jessie talked about his aunt and the raccoon that she used to see.
He mentioned that even after that they killed it, his aunt kept seeing it.
Some time after that, they found out she had cancer
and it was one of the side-effects.
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I thought it could possibly be a role reversal.
Walt was Hank constantly trying to catch the fly and obsessing with it to the point where he was hurting himself and doubting his life which is exactly what has happened to Hank through is obsession with finding Heisenberg.
Also, Jessie ends up killing the fly which could possibly foreshadow Jessie killing Walt.
But that's every unlikely...
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The entire episode reminded me of the "Theatre of the Absurd," which I studied with mild frustration in college: Sartre, Camus, Pinter, Ionesco, Albee.
To paraphrase: '
man is a meaning-making animal, alive in a meaningless universe; ergo, all his efforts are absurd!'
I thought Vince gave the main actors a chance to interact for an entire episode, like Didi and Gogo in Sartre's "Waiting for Godot."
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One of the Breaking Bad episodes involves a scene with a fly. Walter is obsessed by a fly in the lab and tries to kill it in order to keep the room clean.  I was told there's a special meaning but I have no clue about it...
What is the meaning of the "fly scene" in Breaking Bad?
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<plot-explanation><breaking-bad>
movies.stackexchange.com/questions/3339
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According to a review in the Wall Street Journal: The fly has become a symbol of the loss of control in Walt's life, so its defeat is all that's important to him right now. The fly has become a symbol of the loss of control in Walt’s life
The fly has become a symbol of the loss of control in Walt’s life, so  its defeat is all that’s important to him right now.  