What was the ecological disaster?

Self-inflicted genocidal nanobots. Read further to understand why "self-inflicted."

Who built the silos?

The silo project was the brainchild of a US Senator. Through extensive political horse-trading, leverage, dirty tactics, you name it, he was able to secure funding for the silos and oversee their construction. There are 50 or 51 silos in total, outside Atlanta. The cover story of their construction was that they were to provide deep underground storage for nuclear waste. In actual fact they were long-duration isolated habitats to preserve humanity from the fallout of a nanotech war. The initial population of each silo came from a big ribbon-cutting ceremony / political rally / Democratic convention, where reps from each state were in the area around each silo. Atlanta was nuked to provide a reason to get everyone underground, at which point each silo was sealed.

This is the other reason magnification is verbotten in the silos. If the inhabitants got really good at magnification then they might find the killer nanobots outside their door, and then there would be some very difficult questions with no good answers.

The Senator's thinking went like this:

• Nanotechnology is reaching a point where someone could use it as a weapon to kill entire populations based on genetic markers.
• Such a weapon would be almost impossible to stop.
• It is inevitable that someone somewhere will attempt to use such a weapon to wipe out their rivals. No nuclear fallout, no lingering poisons, no destruction of infrastructure, just whole countries depopulated and free for the taking.
• If the weapon will inevitably be constructed and cannot be stopped then we must build it and use it first, before anyone else does.

Nanobots were actually released by the silos themselves after they were first sealed, as well as being released worldwide to kill everyone not in the silos. Whenever the silo doors are opened, additional nanobots are released to keep the area around the silo uninhabitable so that the inhabitants are strongly motivated to stay inside. There's actually one silo not like the others, Silo 1. This silo's inhabitants work in six-month shifts, monitoring the other silos and going into cryosleep between shifts. Silo 1 works with the heads of IT of each other silo, reading them in on part of the history so those IT heads understand the stakes. Of course, the heads of IT are not told that the inhabitants of Silo 1 deliberately caused the disaster in the first place.

Every silo is rigged to blow so that if it looks like its inhabitants have completely escaped control, Silo 1 can remotely detonate and pancake every floor in a silo down to the bottom of its pit. Silo 1 also has bomber drones as a backup, in the event that the inhabitants find and disable the remote detonation capabilities. This is why the head of IT is so frantic to prevent an uprising. He knows that he has to maintain order at all costs, or Silo 1 can literally pull the plug on their silo and all its inhabitants.

So why the head of IT? Because the other part of the plan is the servers in each silo. They maintain records for every silo inhabitant, and Silo 1 has backdoor access to that data. The silo project is also an attempt to prevent a repeat of a nanotech war, by reducing humanity to a homogenous and unified population. At some future date when each silo's supplies are running out, one lucky silo gets told where to find the digging machine at the bottom of their silo. The chosen silo would be the one with the most cohesive population and the best chance of long-term survival, according to computer models and simulations. All the other silos are to be destroyed.