Praulia Massacre

The Praulia Massacre was an event where several second-model supersoldiers were deployed into the Serena Republic to face combat, but due to flaws in their creation, they began killing the population indiscriminately before being put down by newly-deployed Model 3s.

Prelude
The Serena Republic's Delgado regime was formed through backdoor military support by former CIA agents as well as backed by various American corporations. In exchange, America gained various trade agreements with the country, and the specific people involved in his rise to power also gained some special privelages in the country. The shady connections were upheld for a long time, which eventually led to one of these companies, SaintLogic Inc., to conduct a field test with their experimental supersoldiers when the minority Guerilla groups were giving Delgado a hard time. At least two high-ranking officials were involved in this, Rodzinski, the president of the company, and United States Department of Defense Joint Chiefs of Staff General Wiseman, who also orchestrated the entire event. The Model 2 super soldiers were then deployed to quell the rebellion.

The massacre
However, it then ran into a problem: Wiseman, one of the people involved, felt the test data from the quelling of the rebellion was not sufficient enough, so he secretly contacted Lucinda Koppelthorn and other technicians and ordered them to provoke the Model 2 soldiers into going into a violent frenzy. The events led to the deaths of over 10,000 people in the country, which was officially blamed as the Model 2 soldiers being flawed in production. After this, the Model 3 soldiers were deployed into the Serena Republic to eliminate the Model 2 soldiers, one of whom was Snake, a clone of the legendary Solid Snake who had died during the Lobido Incident. However, the events caused the Model 3 soldiers great pain in hurting their brethren. Eventually, a clean up team was deployed, among them Venus, a newer model of supersoldier. She managed to severely wound Snake while he was trying to escape, leaving him with a severe dose of amnesia, and then left him for dead. Likewise, Lucinda was killed while trying to help Snake escape.

Aftermath
Snake ended up surviving the assassination, although with a severe bout of amnesia. He later managed to aid the guerilla groups in overthrowing the Delgado regime, but then he and his allies were forced to flee the country three years later after Escobar murdered Secretary of State Perez and framed them for the deed, an action that was in fact orchestrated by Wiseman so he'd have a criminal in his plan:

Likewise, rumors of the Praulia Massacre slowly became public, with several also requesting that the International Criminal Court look into the case. Because of this as well as his earlier involvement in the massacre, Rodzinski attempted to supply the Lucinda file and rat out his fellow co-conspirators to either clear his name or get a lighter sentence. His conspirators, more specifically Wiseman, became privvy to Rodzinski's plan and attempted to retrieve the Lucinda file in order to prevent Rodzinski from squealing.

Dr. Thomas Koppelthorn, the husband of the late Lucinda Koppelthorn, also was deeply enraged and torn by her demise, and also was led to believe that Snake had killed her. After reviewing the file, he demanded that the ones responsible for the Praulia Massacre be delivered to him, and also revolted and gained Metal Gear Chaioth Ha Qadesh with the intention of launching one of its neutron bombs in three hours should they refuse.