Intercity Transport Gates (転移ゲート or トランスポートゲート) were the main method of teleport between the major cities on a server. However, after the Catastrophe, the gates were no longer active, effectively cutting off each of the major cities from each other. The only remaining option for quick teleport between cities was by Fairy Ring, though since the destination cannot be predicted in a Fairy Ring transport without the use of online charts, they are not a reliable option.
When Elder Tale was still a game, the transport gates were a convenient way to travel between Adventurer Cities, especially for quests. Serara, just before the Catastrophe struck, went from Akiba to Susukino for a quest, but was stranded there due to the unusual event.
Although the transport gates shut down after the Catastrophe due to then-unknown reasons, it was revealed that Minami managed to get theirs' partially working, perhaps through Zeldys' Overskill, Mana Breeder. ReGan, through his research on Susukino's Transport Gate, discovered that they shut down because of a lack of magical power. Like the Fairy Rings and the Cathedral, the Gates were tied to the Moon; combined with the information from Roe2's letter, Shiroe deduces that something, perhaps the Genius, were tampering with Alv ruins there, causing the blackout of the transport gates.
His deduction is ultimately wrong, although he was on the right track: while the Genius were involved with the blackout, they were not directly responsible for it. Instead, Elias Hackblade forced the activation of the transport gate to the Fortress of Apocalypse to allow the Thirteen Chivalric Orders to engage the Genius in battle directly, which drained the energy out of all the other transport gates. Since the Genius were somehow able to escape the seal eight hours before they had planned, and unleashed their Words of Death upon the Ancients, Elias sent the remnants to attack the fortress while he stayed behind to buy time.