Base your reality on films like Man of Steel or Transformers, and there's only one way towering skyscrapers come down: they break in half and fall over as glass shatters and steel bends, taking another building or two down during the collapse. Actual skyscraper demolition is obviously a delicate process, but sometimes they do come crashing down. Demolitions experts blow them up from the inside, carefully planting explosives so they implode and collapse without damaging surrounding buildings. And then there's the Japanese method: Quietly disassemble the skyscraper, piece by piece, so that its disappearance is barely noticeable.
The New York Times offers an interesting look at how skyscraper destruction works in Japan, where tough laws on recycling make implosions impractical. Some skyscrapers are gutted from the top down, and as each floor is completely dismantled, scaffolding obscures the work from the outside. Others are jacked down from the bottom, floors disappearing one by one. The end result, in either case, is that the building looks absolutely normal, just smaller, until one day they're gone.
As much engineering brainpower goes into building a skyscraper, it's hard to imagine the amount of careful planning it would take to disassemble one. The top and bottom methods both offer advantages. Describing disassembly from the top, the Times writes "When the two floors are gone, the roof and scaffold cap slowly descends, thanks to computer-controlled jacks on each of 15 temporary columns. Then the columns are lowered into new positions, and the workers start taking apart the next two floors." Thanks to the scaffolding cap, this method is 20 decibels quieter than a disassembly leaving the roof open, and releases 90 percent less dust into the air.
The bottom-up approach, by comparison, involves "cutting a building’s steel columns at ground level and jacking the entire structure down as each floor is removed. Since all the demolition work is done on or near the ground, there is no need to place heavy equipment, or workers, at the top of the building... Huge hydraulic jacks supported the building’s 40 columns, and workers cut 30 inches from each column, over and over, to allow the structure to be slowly lowered."
The Times goes on to describe how many skyscrapers in New York need to be torn down and rebuilt to offer more accomodations and greater energy efficiency. It's unlikely Japan's methods will be implemented, but implosions won't be used, either--in the non-movie version of New York, implosions and wrecking balls are rarely used due to safety concerns.