The story, taking place in 1957, centers around Jason Roberts, the protagonist and character under the player's control. Although younger, relatively inexperienced and nearly polar opposite compared to his older brother Allen, Jason works together with him at the same company: Allister Research.
Allen is a strong-built and ambitious man, travelling the globe to pursue research for the company, while Jason, 10 years his junior, is fresh out of college and is more of an all-american archetype (for that decade, anyway). For the past several months, Allen has been exploring in the Amazon river basin, but his crew was attacked - no news of his expedition or its crew has been received for weeks.
Once it is learned that the entire crew was killed, except for possibly Allen who is simply missing, it is up to Jason to venture into the Amazon and uncover the mystery of what happened to his brother.