We don't know who struck first, us or them, but we know that it was us that scorched the sky. At the time, they were dependent on solar power and it was believed that they would be unable to survive without an energy source as abundant as the sun.”
― Morpheus to Neo[src]
During the early years of humanity's war against the Machines, the leaders of the United Nations found themselves desperately trying to halt the advancement of 01's armies, who were relentlessly advancing and overrunning various nations in Africa and Eurasia.
When the war begun sometime after 2139 (approximated based on the end of the Second Renaissance), the Machines were steadily winning against humans. Looking for any way to slow their advance, scientists devised the plan to block the sun's rays from the surface of Earth using nanites sprayed into the upper atmosphere in the hopes of cutting the Machines off from their primary power source.
This "final solution" was codenamed Operation Dark Storm.
So the leaders conceived of their most desperate strategy yet, a final solution - the destruction of the sky. Thus would man try to cut the Machines off from the sun, their main energy source.”
― The Instructor[src]
The operation commenced with UN bombers deploying the shroud over Eastern Europe, which soon encircled the entire planet. While the humans were successful in "scorching the sky", Operation Dark Storm carried tremendous costs both for the planet and humanity itself. Without energy from the Sun, much of Earth's life did not survive, leading to the total collapse of the biosphere.
Universal crop failure soon followed, causing worldwide famine. A vast amount of human military equipment which heavily relied on solar power was also crippled. The operation soon proved to be an absolute failure, as the Machines were able to adapt to a world without solar power. Humanity was ultimately defeated and placed into the virtual-reality world of the Matrix.
Even after dominating the planet for nearly six centuries, the Machines had not been able to remove the nanite shroud. The Architect's revelations to Neo suggested that their current year was actually somewhere closer to 2699, which meant that even with all their advanced technology, the Machines had been unable or, conversely, unbothered to remove the nanites.
Some parts of the planet were radiated. And some were stuck in eternal rain. At the edge of all the ruin, where the land was endlessly wet and left alone by Machines, non-human life survived. Wet weeds, trees, forests, and water-loving plants remained green. And fungi, ducks, frogs, slugs, rats, and cockroaches continued to thrive near them. All of this despite the scorched sky, which made photosynthesis impossible.
Additionally, Geoffrey, sometime at the beginning of the sixth Zion, was able to discover and propagate genetically-modified wheat seeds from the world prior the war, which eventually gave rise to the growth of wild wheat fully-adapted to the unceasingly sunless and rainy skies.
Towards the end of the war (approximately, on the year 2699), Neo and Trinity briefly flew the Logos over the nanite shroud. This caused not only the heavily damaged hovercraft to stop working but also deactivated all of the sentinels attached to the hull. While this suggested that the Machines were not capable of bypassing the shroud, the Machines were entirely capable of space flight and, at some unknown point before or after the sixth Zion, had regularly sent Machine probes to space.
- Mahiro Maeda's Behind the Second Renaissance, matrixfans.net
- Operation Dark Storm is described in The Second Renaissance, a two-part short film from The Animatrix.
- Morpheus tells Neo that he did know that man was the one who "scorched the sky", showing him a depiction of the Earth's sky while introducing Neo to the concept of the Matrix within the Construct.
- Matrix Beta Versions, Zion was the sixth reincarnation of itself, having been wiped five times before in an estimated cycle of once every century
- The Miller's Tale
- A Sword of a Different Color