Following his Army career, Wesker was reassigned by Umbrella in 1996 to serve in S.T.A.R.S., a private-funded police special forces unit in Racoon city. The special tactics and rescue service was effectively Umbrella's private army, nominally raised to deal with the increasing threat of domestic terrorism in the American heartland, and earning them a direct source within the Racoon City Police Department should an investigation linger uncomfortably close to the company. He was made Captain of the Alpha Team.

For the next two years, Wesker worked closely with fellow Alpha Team teammates Chris Redfield, Jill Valentine, Barry Burton, Brad Vickers and Joseph Frost as their Captain as a means of earning their trust to maintain his cover. At some point Wesker and the other S.T.A.R.S. members began a joint project with their exclusive arms supplier Gun shop kendo to develop each stars member a specialized samurai edge handgun, which each member supposedly getting their own exclusive variant to suit their needs with Wesker designing most of the modifications for his own Samurai Edge himself.

Betrayal (1998)

"I will follow my initial plan and lure the S.T.A.R.S. members into the Mansion. Their superior combat training should make them perfect test subjects."
—

The Spring and Summer of 1998 saw considerable upset to Umbrella in Raccoon City. The new E strain infected a number of staff at the Arklay Laboratory in May, prompting a quarantine of the staff while its guards made preparations to shoot all escapees. Wesker and Birkin personally visited the lab shortly after the alarm was raised to evacuate the cloned embryos of the T-002 tyrant, one of Umbrella's most important assets. Wesker also gave orders to forbid phone calls in order to limit the spread of information.

Escaped Cerberus B.O.W.s did however escape their cages and began killing and attacking civilians in Racoon forest, with infected survivors going on to kill others. By July the number of killings had surpassed 20 civilians in what the RPD theorized to be the work of a cult. Unable to locate suspects and/or any logical motives public outcry grew to fever pitch. After the lack of results of an extensive dragnet by Raccoon Police and after press backlash, the RPD assigned the case to S.T.A.R.S. No longer able to manage the situation from within Umbrella HQ produced the "X-day" plans, giving Wesker a series of tasks to perform during the mission. He received orders to sacrifice S.T.A.R.S. to the mutants to provide combat data, eliminating them as witnesses; to collect the remaining B.O.W. embryos, and to finally destroy the Arklay Laboratory itself to wipe out all trace of the virus. On 23 July, Wesker sabotaged the engine of Bravo Team's helicopter, which would prevent their escape and require Alpha Team's subsequent investigation.

Wesker and Birkin planning to leave Umbrella.

During the S.T.A.R.S. preparation, Wesker and Birkin also had other duties with the company and was to oversee the reopening of the executive training school, possibly to make up for the loss of the Arklay Laboratory. An attack by a nascent mutant leech colony destroyed two armed investigation teams and infected the occupants of a private train taking key personnel to the school. To prevent the outbreak spreading out further, the two made plans to blow up the training school. While there, Wesker encountered Col. Sergei Vladimir, the executive in charge of the UBCS, after Umbrella HQ took notice of the incident. Wesker escaped from the facility before its destruction, but his experiences in the night convinced him abandoning Umbrella was now essential. He agreed to a rival company's offer of employment in exchange for giving them the embryo samples rather than handing them over to Umbrella.

On the evening of 24 July, Wesker led Alpha Team out to the mountains as he had expected. To better his chances of survival, Wesker was provided with a mutant strain designed to mutate his body to enhance his strength and regenerative abilities. Soon after arriving at Bravo Team's helicopter site, where RPD pilot Kevin Dooley's body was discovered, the team was attacked by the Cerberus pack and Joseph Frost killed, with pilot Brad Vickers abandoning the group in a panic. After saving Chris from being attacked by a Cerberus, Wesker and the surviving members fled to the nearby Spencer Mansion to seek shelter. Inside, Wesker separated the team into groups to investigate different areas of the house. He also threatened Barry Burton with the nonexistent threat of his family's murder, forcing him to assist in the confiscation or destruction of incriminating evidence. Wesker discovered Captain Enrico Marini to be alive and having incriminating evidence against Umbrella and promptly shot him in the underground tunnels before fleeing.

Wesker wakes up soon after his “death".

In the lab, Wesker began preparations for waking up the Tyrant to kill the remaining S.T.A.R.S. survivors, infecting himself with the mutant t-virus strain shortly before doing so. He was cornered by his comrades while in the chamber and confessed his role in Umbrella's conspiracy before ordering the Tyrant to attack them. However, T-002 recognized Wesker as a participant in the Tyrant Project, and he stabbed Wesker first, impaling him through the chest before going after the others. Though Wesker was seriously wounded, the virus in his body had succeeded in mutating him to possess impressive regenerative abilities, and he woke up in an empty room. With the self-destruct system prematurely activated and his computer access restricted by Col. Vladimir and the RED QUEEN AI, Wesker was unable to recover the embryos or any important data to hand over to Umbrella's rival company. He narrowly escaped the destruction of the mansion after a fight with Lisa Trevor, but his improved speed ensured his survival. Believed dead by Umbrella and S.T.A.R.S., Wesker was able to gain employment within the company despite his failure to provide the samples.