The system is run on Midgar Standard Time, with the system threaded throughout the city's upper plate and linked to a neglected Train Graveyard in the city's slums via a giant circular track that spirals up the city's central pillar. These rail systems are heavily monitored by the city's security system, with various security checkpoints along the routes used to automatically scan the ID cards of the passengers. An invalid ID results in the train being locked down car by car.
Another train can be seen at the Sector 1 Station, which links to the Sector 5 Slums with Sector 8. The train is called the MK93 II, however, a boy at the platform says that an even newer model, the MK100-90, is in the works.
As the professor is carrying classified materials on SOLDIER, and so is a highly valuable target, a small unit of Shinra Military troops are also issued to ensure her protection; amongst them a young trooper called Cloud Strife.
The Midgar train system is used by Cloud Strife and the members of the reformed AVALANCHE group to enter Sector 1 and bomb the Sector 1 Reactor and later used to escape the scene; using fake ID cards, they then returned to the Sector 7 Slums.
Each sector in Midgar has at least one train station, making a total of eight stations used by passengers to embark and disembark at various points in the city proper.
In the Midgar slums there exists at least one station, which is also linked to the Train Graveyard.
- There are also abandoned rail systems running through Mt. Corel; an abandoned mining location and site for a destroyed Mako Reactor, but are only used once by Shinra in Final Fantasy VII in an attempt to transport a Huge Materia from the location. Cloud's party, temporarily lead by Cid Highwind, attack this train to save the Materia. The train then goes out of control. Depending upon the player's actions this train can be stopped or it will crash into the town of North Corel.
- Although it is revealed that the train was part of a holographic training simulation, the opening scene of Crisis Core -Final Fantasy VII- mirrors the start of the original Final Fantasy VII.
- The opening scene of Final Fantasy VII is later remade as a technical demo of the PlayStation 3's graphic system.
- Built underneath Midgar, Deepground has a separate monorail system that ferries people through the underground city to various locations.