SOLDIER was disbanded sometime before the game but it baffles how can disappear overnight. Some were enemies in the game, some had become Sephiroth's followers and some went into Deepground but whatever the rest of SOLDIER?

Taken from Final Fantasy Wiki


Approximately 30 years before the beginning of Final Fantasy VII, the Jenova Project was initiated to make a human-Cetra hybrid using the cells from Jenova (mistaken to be a Cetra) and Mako Energy from the Planet. The result of this experiment was Sephiroth, a child with exceptional abilities. Shinra recognized the potential of such a powerful warrior, so a method was planned to begin a mass production of more fighters of his type.

Using similar processes, Shinra began exposing promising warriors to raw Mako (giving their eyes that unique "glow"). Despite Cloud's dream of becoming a SOLDIER First Class, he lacked the mental strength to make it through the Mako Infusion, so he never did join the organization. Although still eclipsed by Sephiroth's strength and power, these new warriors called SOLDIER were given powers far beyond those of a normal combatant. They were sent on the more dangerous or important missions, had access to more equipment and information, and were higher ranked than other members of the army. These forces would be used to great effectiveness during the Wutai War.

AVALANCHE

During the battles with the first AVALANCHE in Before Crisis -Final Fantasy VII-, the data on SOLDIER operatives are stolen. Fuhito, expanding on the SOLDIER idea creates his own brand of super soldiers, the Ravens. These forces are completely without wills; they are only mindless killing machines. Using the SOLDIER data, AVALANCHE is able to predict SOLDIER movements, and capture several members to transform into Ravens. The SOLDIER force never successfully defeats AVALANCHE, with most of the battles fought by the Turks.

Mass Desertion

Headed by the SOLDIER Union Executive, Lazard Deusericus at the time of Crisis Core, SOLDIER acts from the Shinra Headquarters in Midgar, from floor 49 where there is a training room, briefing room, and lounge area for off-duty members. Most SOLDIER members seem to spend their standby time here, wandering and talking to each other. Materia synthesis seems to be closely related to SOLDIER, as the room where it is made from crystallized MAKO Stones is also on the SOLDIER Floor.

However, many Second and Third Class SOLDIER's suddenly disappeared along with First Class SOLDIER Genesis Rhapsodos. Shortly after the desertion, Angeal Hewley, also product of the Jenova Project like Sephiroth and Genesis, leaves the organization. Angeal was the emotional heart of SOLDIER, acting as a mentor to the younger SOLDIERs and inspiring them to always hold on to their "SOLDIER honor". Once these two were gone, Zack, who was Angeal's prot�g�, was promoted to First Class and takes up Angeal's role as heart of SOLDIER, using many of his same lines. Later Lazard defects to join with Genesis, causing great chaos across the Planet. Zack and Sephiroth are sent to Nibelheim to fix the Reactor there. During the mission, a series of events result in Sephiroth denouncing his humanity, and destroying the entire town. After Zack is defeated by Sephiroth, a young Shinra Guard, Cloud Strife defeats him. Zack and Cloud are taken by Professor Hojo as test subjects in the next round experiments in the Jenova Project. Though Zack later escapes, taking a Mako poisoned Cloud with him, he is gunned down by the Shinra army just before reaching his destination, Midgar.

The Fall of SOLDIER

In Final Fantasy VII, while SOLDIER itself plays an important role in the story, actual members of SOLDIER are few and far between. This could possibly be attributed to the loss of personnel after the mass desertion, the disappearance of the Director of SOLDIER, and the loss of SOLDIER's three most prominent members (Genesis, Angeal, and Sephiroth). The appearances of SOLDIER members in the game are limited to enemies encountered during random battles and include SOLDIER 3rd Class members guarding the Shinra Science Department area on floors 68 and 69 of the Shinra Building, 2nd Class members that are stationed in Junon after Meteor is summoned, and SOLDIER 1st Class members guarding the Mako Cannon in Midgar. Cloud claims to have been a member, but this is a false memory created by the physiological damage Hojo's horrible experiments caused him as well as the trauma he experienced from the destruction of his hometown, and the death of his best friend, Zack. Even though Cloud was never a member of SOLDIER, he becomes strong enough in Final Fantasy VII to be mistaken for a 1st Class member. Because of the experiments, Cloud's eyes have the "glow" that makes people believe that he was a former member. After Shinra collapses, SOLDIER seems to have fallen with it. However, during the events of Dirge of Cerberus -Final Fantasy VII-, Vincent encounters remnants of SOLDIER hiding out in the Shinra Mansion and in the ruins of Midgar.