The Fortress is created from a nano-crystal that Jor-El enclosed in Kal-El's spaceship. The crystal leads teenage Clark Kent to the Arctic Circle where, after he throws it down, it melts into the ice and grows into a huge crystalline building. The Fortress possessed all of Krypton's history, culture, philosophy, Science and religion. Clark lived for four years at the Fortress where he had been training in the use of his new powers and learning his Kryptonian heritage.
After Superman finished his training, the Fortress was discovered by the X-Men when Professor Charles Xavier detected Superman's power signature. It is here that Superman first met the X-Men and decided to join them. However, he has returned to the Fortress as time went on to work on various Kryptonian technology, either continuing Jor-El's work to complete old projects or carrying out upgrades and repairs on salvaged Kryptonian resources.
Despite the Fortress's secrecy, the Fortress became the site of a diplomatic crisis between the surface and Atlantis as its presence violates a established Atlantean treaty in which the Arctic was declared an Atlantean territory due to being the last great depository of fresh water supplied for Atlantis. King Namor believed the Fortress posed a threat in polluting the Arctic and had Atlantean warships prepared to fire on the structure; however, Superman reasoned that the Fortress doesn't endanger the Arctic and even allowed the Fortress to be fired upon to display its advanced defense that cannot be remove even by force. Superman and Namor came to a truce in which the Fortress would be also protected under the jurisdiction of Atlantis, based on the likelihoods that their respective enemies would eventually try to endanger the Fortress.
Over the course of time, it has been the target of numerous organizations, criminal or otherwise, due to the advanced technology and secrets that lie within it. Project Cadmus and later HYDRA captured Alison Blaire, Superman's lover, and tried to torture the access codes to the Fortress out of her; Quicksilver, on orders from Magneto, made a futile attempt to get inside the fortress; Doctor Doom has repeatedly attempted to gain entrance to it (To the point that he created a clone of Superman to try and breach the defences); the Kree, Skrull, and Shi'ar launched a full-scale invasion of Earth in an attempt to seize it.
- In DC Comics, in Pre-Crisis continuity, the Fortress of Solitude was located at the North Pole, and the Fortress as seen in the films Superman: The Movie and Superman II are likewise located at the North Pole. In Post-Crisis continuity, the Fortress are located in Antarctica.