He was sent to an undefined (Spanish-speaking) South American country situated within the Amazon rainforest, where he was to meet up with Kennedy by his means, choosing to pay a man to drive him to the rendezvous coordinates.[6] Jack was unable to meet Kennedy by his initial choice of transportation due to a sudden riot taking place in a town along the route, leading to roadblocks being put in place. Not permitted to return fire on the riot police for their use of armed violence against the individuals, Jack was forced to continue on his trek already ten minutes late. Faced with a large river obstructing his journey, Jack was lucky enough to hitch a ride on a freight train running nearby.[8] Eventually, Jack met up with Kennedy at a nearby town along the train route; while Kennedy had made it there on time, his tour-charted Cessna had been shot down along the way.[9]

After meeting Kennedy, the two moved out through the rainforest to their mission, which was later revealed to be a Presidential order to limit the spread of the t-Virus and the selling of Bio-Organic Weapons. Their targets were Javier Hidalgo, a wealthy local drug lord, and an Umbrella researcher who was selling bio-weapons products to him. Krauser and Kennedy have been sent on a mission by the U.S. government to infiltrate Javier's mansion in a small locale of Amparo. Finding Javier is their objective since he is a drug lord who has taken de facto control over a large area of jungle. He rules the entire area. The small government is unable to do anything about Javier's control of the drug trade, so Krauser and Kennedy have been called in.

The U.S. government has received information that a former Umbrella researcher has somehow entered the region. Sources indicate that something strange is going on, but no accurate information can be obtained. Unwilling to risk a biohazard incident, a secret military agency pairs Kennedy and Krauser and sends them into this volatile region to determine what, if anything, is going on.

Shortly after they arrive at their drop point zone (the Jungle), but before arriving at the village of Mixcoatl, Krauser tells Kennedy that he doesn't believe in B.O.W.s. Kennedy speculates that he sees the Enemy as being the same to him.

They found themselves having to cooperate as a two-person cell in a t-Virus outbreak. During their cooperation, he becomes more interested in Kennedy's experiences in the Raccoon City Destruction Incident. After learning as much from Kennedy as he can, he realizes that the enemy they are facing is entirely new to him, and thus starts to realize that B.O.W.s do indeed exist. Upon arriving within Mixcoatl, Kennedy and Krauser are faced by the zombified residence of the village, before finding their guide mortally wounded as well. They soon struggle past the various B.O.W.s which they encountered, only to find a mysterious girl, named Manuela Hidalgo, along with a fierce amphibious B.O.W.[10] which they soon manage to defeat for the time being.[7]

Kennedy and Krauser are guided by Manuela through Javier's massive dam, only to encounter even more B.O.W.s. They then learn that the young girl is Javier's daughter, and had been infected with the Veronica virus, before being separated from her by Javier's men. As Kennedy and Krauser eventually struggled through the dam and met up with Manuela yet again, they learn that she was administered the virus to save her from a terminal illness which she and her mother contracted, with Manuela agreeing to take them to her father's mansion.

Along the way, Krauser, concerned about the possible transformations which Manuela could undergo due to the Veronica virus, learns of Kennedy being sent into this mission under the direct orders of the President, to eliminate the virus. Although Krauser agrees to help Kennedy, deep down he begins to feel jealous, almost spiteful, of Kennedy's elite status, as well as starting to doubt and reservations whether the US government brushed him aside, with him also desiring to complete the mission to prove his self-worth to the government.

As the two make their way through Javier's mansion, Krauser continues to contemplate the mission. He soon finds himself agreeing with Javier's mentality of "becoming stronger to survive," and he grows increasingly resentful of Kennedy. This leads Krauser to become obsessed with the power of the Veronica virus.

As the three make their way down to a warehouse, they find the truth about Manuela's control over the virus: She has her vital organs regularly transplanted from kidnapped girls to both reduce the pain of the virus and to keep her mind strong. Javier then sends out the same amphibious B.O.W. which Krauser and Kennedy encountered earlier, only to find that Manuela can keep it from attacking by singing. As they try to protect her, Krauser ends up having his left arm impaled by the beast, severely wounding him, before he and Kennedy learn that the B.O.W. is Manuela's mother, Hilda.

As Javier merges with the Veronica Plant, becoming the "V Complex" bioweapon, Kennedy, Krauser and Manuela work together to defeat it. All the while, Krauser becomes more and more convinced that the power of this virus is beneficial, and that destroying it would be a mistake. He thus becomes fully convinced that he must become stronger, viewing Kennedy as a "coward", and deciding that he will become more powerful.

Krauser training Kennedy prior to Operation Javier.

According to another account, Krauser was tasked in training new recruits in the top secret government program, putting them through grueling training that transferred his knowledge and wisdon in close-quarters combat and battle. One of the recruits was Leon Scott Kennedy, who Krauser took particular interest in.