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The machines turned to using humans as a source of power after the humans darkened the skies, since the machines relied on solar power before.

If the machines were smart at all, they'd realise that their strategy is unsustainable, since energy on Earth predominantly comes from the Sun in some shape or form (i.e. plants, oil, coal). So why would they not invest into penetrating or even getting rid of the clouds?

The 3rd movie clearly shows that it's possible to penetrate the cloud layer when Trinity flies through it. Although there was an issue with the lightning interference, hey, they survived! And I'm sure they can either build some sort of shielding, or even harness the lightning to their advantage.

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    A better question: Why didn't they simply fly into Space? – I Love You 3000 Jan 29 '15 at 19:01
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    Taken the premise of human batteries for what it is - utterly flawed - and we also have to assume that the machines are perfectly aware of this, there's only one choice: Nested layers of the Matrix. Zion-World is another form of the Matrix, so darkened skies do not matter and are just for the show. The real "real world" is one level further up and got free skies, solar power and whatnot the machines desire. The Dual-Layer-Matrix is not powered by humans but is nothing more than a hamster cage. AI keeps humans as pets. Resolves all energy troubles and even more so some plot holes of the 3logy. – Ghanima Jan 29 '15 at 20:13
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    @ArturoTorresSánchez, go again, what shall I do? C'mon, the pivotal premise of the Matrix is flawed beyond description. And how is it never hinted in the movies? Stopping sentinels in the "real" world? – Ghanima Jan 29 '15 at 21:13
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    A recursive Matrix is the only explanation for how Neo had any powers in the "real" world. It isn't the real world. – David Conrad Jan 29 '15 at 21:36
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I don't think an answer is ever explicitly stated in the canon, but we do have two pieces of evidence that hint at an answer:

First, we know from several sources, most importantly the animated short The Second Renaissance, that the sky was darkened WELL before the war with the surface (that is, pre-Zion) humans was over. From this we can assume that any attempt to gain electricity from above the cloud layer at that time would have been the immediate target of attack, and thus not worth making.

Second, Morpheus's line from the first movie is quite telling:

Combined with a form of fusion, the Machines had found all the energy they would ever need.

It seems that, realistic physics aside, the Matrix is a source of energy so abundant that any other system would be unnecessary. That is, they simply don't need to look for other sources of power.

Given those clues, all indications point to the idea that they developed a war-time solution for their power needs, and that solution was so effective that they simply haven't needed to change it ever since.

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    Actually in the Matrix story "Goliath", we learn that they've been extensively exploring space. Something nasty follows their probes back to Earth. – Valorum Jan 29 '15 at 19:25
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    I love that "combined with a form of fusion" remark, as if it's insignificant. I can move a 2-ton car at 80mph just by pushing with one foot, combined with a form of combustion. – KSmarts Jan 29 '15 at 19:39
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    @KSmarts True, but I think it's safe to assume that, given its importance within the world of the franchise, the Matrix is a significant source of energy, probably the primary source of energy for the Machines. It doesn't work in real physics, but then neither does the rest of the story. – Nerrolken Jan 29 '15 at 19:43
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    So a species could have a better, more efficient fuel source, but because their existing infrastructure met their needs (even though it isn't sustainable in the long term) they didn't invest in that better fuel source. It's like these machines were programmed by humans or something. – corsiKa Jan 29 '15 at 23:02
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    Part of the problem here is that (supposedly) the original concept humans were being used as essentially coprocessors rather than batteries, but focus testing concluded that not enough people would understand it and so they switched to 'batteries' despite it making no sense vis a vis the laws of thermodynamics. – Shadur Jan 30 '15 at 13:44
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The screenplay for Matrix Revolutions makes it abundantly clear that the clouds unleashed in 'Operation Dark Storm' are comprised of "molecular replicators" which are totally hostile to the machines. When entering (or even approaching) the cloud layer, the sentinels are instantly "drained of life", then struck by bolts of high-powered lightning.

We can assume that any attempt to dismantle this layer would be a monumentally difficult task. Not only would they be unable to even approach the clouds but since the layer is comprised of "replicators", it seems pretty likely that when you try to destroy them, they ... y'know ... replicate...

Scene 737 : EXT. BLACK SKY - NIGHT

Rocketing towards the churning black sky, leaving a white-hot jet trail that cuts up from the black earth at a forty-five degree angle.

Several Sentinels leap from the back of the ship, but many remain as it barrels towards the dark roiling ceiling.

The Logos plunges into the sky with a surreal splash, like a plane crashing into a sea of shaving cream.

The molecular replicators immediately drain the life from the Sentinels and they fall dead tearing through the clouds that cling to them momentarily like shredded pieces of parachute, before letting them fall away.

The Logos is engulfed by a ball of lightning as it is attacked by the sky. It shakes violently, every light blowing out, until the ship dies

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    Note that in the webcomic GOLIATH, we see that the machines have made forays into space. That said, if you consider this to be canon, it doesn't change the second part of the answer. – Valorum Feb 6 '15 at 9:19
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    Those replicators sound handy. Why did the humans leave them all in the sky? – Praxeolitic Feb 21 '15 at 12:31
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    @Praxeolitic - Good question. They seem quite aggressive toward human technology too. – Valorum Feb 21 '15 at 12:43
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There are really 3 Theories that fit within the Matrix Canon

  1. They really need the energy
  2. They still function because they need the humans for something else
  3. they still function because they were created to service the humans(or care for them/protect them)

As we can see from other questions and answers, they can get the energy from Fusion that would be more than sufficient.

The other 2 theories mean that the Machines need to keep the Human race alive for....

  1. Processing power
  2. Protection
  3. Self Preservation

Who knows, could be something dumb like they have a funny obsession with Humans.

But this would mean that they don't need to clear the skies, maybe there is something in space that they are protecting earth from and the skies keep them from scanning the surface to find strategic targets.

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    As I said in my previous answer, the reason why the machines don't simply kill all the humans is because they accepted our surrender (see Second Renaissance, Part II). – Valorum Jan 29 '15 at 19:32
  • Yeah, Maybe they interpreted a phrase in the surrender literally. "let humans live" or something. It can't just be that they need heat from mammals, otherwise elephants would be way more efficient than humans. – Dan Shaffer Mar 28 '16 at 11:48
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Curiously enough, the machines might still obey the Laws of robotics, i.e.

  1. A robot may not injure a human being or, through inaction, allow a human being to come to harm.
  2. A robot must obey the orders given it by human beings, except where such orders would conflict with the First Law.
  3. A robot must protect its own existence as long as such protection does not conflict with the First or Second Laws.

Maybe similar to i, ROBOT they figured that the only way to protect mankind from its destructive nature was to leave the sky dark and keep the humans in the Matrix so mankind were never tempted to try and wage another futile war against the machines.

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Humans still use 'oil' based technologies as our world's major power source, despite there probably being much more efficient, clean technologies available were we to invest as heavily in them. Maybe like us, the 'machines' are being held to ransom by sub-sets of their own kind whom are unwilling to give up their personal power/wealth for the benefit of their species! Greed is surely not only a human foible.

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I remember seeing an explanation on another site that said that the machines were very vulnerable to the electric generated by the nanobots that constantly blanketed the sky(the scortched sky was actually being done by tiny robots that kept scorching the sky whenever it would start to regenerate). We all saw the sentinals get powered down from the electric from them in "Revolutions"
Apparently the machines could never find away to properly insulate themselves from that.

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