Ground Zero is the name given the remains of the World Trade Center following the terrorist attacks on September 11, 2001. It was the largest attack on US soil to that date with the loss of over 3000 lives. The site was utterly destroyed when two separate commercial airliners, commandeered by Al-Gaeda terrorists, flew the planes into each tower. The heavy structural damage caused by the crashes and resulting explosive fires caused the structural integrity of the buildings to collapse.
For years after, Ground Zero was a memorial site commemorating the loss until a brand new building, One World Trade Center, was constructed. One World Trade Center opened to the public in November 2014.
On Earth-616 the attacks on September 11, 2001 happened in a fashion similar to that in the real world. However, the Sliding Timescale of Earth-616 pushes time forward. As such any references or depictions of this tragedy occurring during the Modern Age of Heroes should be considered a topical reference. As of 2016 the Sliding Timescale has moved forward enough that the Modern Age (starting with the birth of the Fantastic Four) did not begin until the year 2002.
The site of the events of September 11, 2001, where Spider-Man and many other heroes worked side-by-side with the rescue crews. Later, there was a conflict between the citizens over the place, some wanting it to remain untouched as a tribute to those who died and some wanted to construct there as a symbol of healing. Eventually, a riot broke up there between both fractions, the police and Commander Steve Rogers, accompanied by Sharon Carter. The riot was so violent that Rogers investigated if there was any supervillain behind it, however, he didn't found anything. It's unknown if the protests have stopped or if any side won.