(Capcom's primary storyline)
"Does he know that Wesker was my father?"
— Jake to Sherry about Chris Redfield
Jake Muller (ジェイク・ミューラー Jeiku Myūrā ) was a mercenary raised in Eastern Europe. The son of bioweapons developer Dr. Albert Wesker, he was dragged into a conspiracy to launch major terrorist attacks with the C-Virus.
Muller was born in a single-parent household in Edonia. Previously an emigre to the United States, Muller's mother returned to her home country pregnant, having broken up with her partner Dr. Albert Wesker, then an Umbrella intelligence agent, who was unaware of his son. As she still loved him, Muller was raised to respect his father, who he privately considered a "dead-beat". When his mother fell ill sometime in the early 2000s, they fell into arrears. Seeking a means to support her, Muller entered work as a mercenary, possibly starting with the Edonian Liberation Army, in 2007. Unskilled, he was quickly drilled by an instructor to taught him not only to fight, but to trust and support his unit.
Travelling across the world, by 2009 Muller was operating in South America with the same unit. It was wiped out in an ambush, Muller surviving by fighting hand-to-hand with one of the attackers, himself armed with a knife. When it was discovered the ambush occurred because their trainer sold them out, Muller lost his faith and trust in others, and for the next three years built up a reputation in not caring for the ideologies of those he fought for, only caring about the money. Working for various paramilitaries including those in the Middle East, Muller built up a reputation for his lack of conviction.
"Yeah yeah yeah, good for you, but... now's not really the time. You coming?"
— Jake preparing to leave after meeting Sherry
By 2012, Muller had returned to Edonia to assist the Edonian Liberation Army, which was dependent on mercenaries in its campaign to overthrow the government in its civil war. Unaware at the time, Muller was carefully being investigated by both the US government and The Family, an American-based organisation involved in bioweapons development. The Family sought to capture Muller to serve as a test-subject for C-Virus research in using his antibodies to naturally select mutant strains that could be superior. The US government meanwhile sought after Muller as his antibodies were crucial in vaccine research.
On 24 December 2012, Dr. Carla Radames - a Family researcher - made her way into Edonia and provided C-Virus samples to the ELA militants under the deception they were nutritional supplements. As expected, Muller injected himself with the sample and his antibodies fought it off, making him immune. The other ELA militants however mutated into J'avo and began purging uninfected humans from their ranks. Muller was soon met by DSO agent Sherry Birkin, sent by the US government to evacuate him for the vaccine research, which he agreed with on condition of a $50 million settlement paid in cash in exchange for one pint of blood. The two made their way through the war-torn city, pursued by a B.O.W. called Ustanak, with orders to capture him. Reaching the ELA-controlled city hall square, Muller and Birkin ran into BSAA forces led by Cpt. Chris Redfield, and fought alongside them in fending off two Ogromans.
Following the destruction of ELA anti-air batteries, the BSAA was ensured air superiority over the situation. When reinforcements were dropped at the city square, Muller and Birkin boarded a Chinook heading out of the city. It was pursued by The Family's helicopters along with the Ustanak. Despite desperate resistance, two BSAA helicopters and their pilots were lost, and Muller and Birkin survived dropping to the mountains with a torn parachute. On landing, Muller discovered Birkin was a mutant capable of regenerating serious wounds, which she later explained as being the result of being infected by her father who died years ago. Tracked down by the ELA's mutant mountain troops, the two were forced to escape from their cabin shelter and skied along the mountain, soon pursued by an avalanche. Making their way into a mine, they were stalked once more by Ustanak, and were successfully captured and handed to Dr. Radames, who revealed to Muller her knowledge of his father.
"If he is half the man you say he is, he'll be fine. OK?"
— Jake to Sherry, about Leon
After six months of being experimented on, Jake was being escorted by several J'avo to an unknown location, a few moments later Jake paused, much to the annoyance of one J'avo. While one of the J'avo was unlocking the door to continue the escort, Jake attacked two J'avo with another's firearm before snapping the J'avo's neck, he then uncuffed himself and proceeded to finish off the others, after finishing off the stragglers he then deactivated the power in order to continue his escape.
While making his escape Jake assisted Sherry several times via security turrets, and soon found his way into a locker room mere moments after Sherry. There the duo began to get changed from their medical apparel into clothing from the lockers and proceeded to arm themselves, during this time Jake asked Sherry if she's familiar with Albert Wesker and he discovered that she was, he mentioned that Wesker was spoken about numerous times and expressed his disgust that his father was a "freaking nutjob who almost destroyed the world". Jake mentioned that he believes he acts like he does due to his father's actions, even asking Sherry if she doesn't think crazy runs in his family and he mentioned his actions make some sense to him now. Sherry, disgusted with his words, scolds him, saying he can blame his father all he wants, but he has to take responsibility for his own actions.
Upon exiting the locker room, the two of them found themselves in a rather lavish living quarters for the facility. They also figured out that they were in China. Wanting to contact her superiors and inform them of their situation, Sherry and Jake searched for a terminal where they could establish a line. Upon finding a computer with data of Jake's biology and a potential cure, Sherry copied the data to a card and took it with her. They also found Sherry's phone, and she contacted Simmons, finding out that he was already in China.
Escaping the facility, they took a motorcycle into the city, with an enemy helicopter in hot pursuit. With the help of Chris Redfield and Piers Nivans, who were also in China, they took down the helicopter and went on to meet up with Simmons at the rendezvous point. While running through the backstreets and alleyways, they came upon a large group of J'avo and fought their way to a clearing where the Ubistvo was knocked down from a train by Ada Wong and landed in front of them. The creature attacked them with its razor sharp arm and attempted to kill them, but the duo quickly gunned it down. Believing it to be dispatched dead, they proceeded onwards.
On their way, Sherry and Jake witnessed a plane crash, Sherry apparently noted that it was American. Upon investigating, they found Leon S. Kennedy along with Helena Harper. After a brief reunion, Sherry told Leon how she was on protective detail and inquired as to why he was in China. Leon revealed to her that her boss, Derek C. Simmons, was the one responsible for the global outbreaks. Taken aback, Sherry did not believe it at first, insisting it couldn't be possible as she reported to him and trusted him. Tensions rose as Leon tried to pressure Sherry into revealing Simmons' location, but Jake stepped in violently. Pulling Jake away, Sherry told him that Leon was one responsible for helping her survive during the Raccoon City incident, which convinced Jake, albeit hesitantly, to trust him.
Sherry's reunion with Leon was cut short as the Ustanak, standing upon the wreckage of the crashed plane, suddenly attacked. The four of them fought against the violent B.O.W., and foiled its attempts to kidnap Jake. After doing what they could to keep Ustanak at bay, the monster finally retreated, but not before a large electrical tower began to crash down. The tower separated the two parties, and Sherry tried desperately to tell Leon and Helena where the rendezvous point was before a massive explosion. With no other choice but to hope that Leon heard her, Sherry and Jake went to continue their journey to the rendezvous.
Using a river raft to travel across water, the two dangerously sailed into an ambush, where the Ubistvo that they had seemingly defeated earlier returned for some revenge. Just when they began to think they were doomed, a gunshot sounded out and hit the Ubistvo. Surprised and unsure if the bullet had been from a friend or foe, Sherry and Jake evaded the Ubistvo as best as they could while the mysterious sniper helped them. After shocking the creature and knocking it into the water, Sherry and Jake once again attempted to flee using another raft. However, the Ubistvo barged on to their raft and almost knocked Sherry into a propeller from nearby debris when the mysterious sniper saved them one last time.
Sherry warns Jake about Simmons' intentions. Finally making it to the rendezvous point, Sherry hesitated outside the door, admitting to Jake that if things went bad, she wanted him to escape, no matter what. (Jake was the world's only chance of creating a vaccine for the C-Virus, due to the antibody he inherited from Wesker.) Jake agreed, though not easily, and the two entered the door, finding themselves in the presence of not only Simmons, but also Leon and Helena.
Simmons ordered Sherry to take Leon and Helena into custody, but Sherry refused, instead asking if what Leon had said was true and if Simmons really was responsible for the bioterrorist attacks. Angered by her suspicions, Simmons revealed that the president had been killed and that Leon was responsible. Helena and Leon quickly rebutted, and a fire fight soon ensued. Sherry, confused and unsure of what to believe was also fired on by Simmons' men, and Jake quickly knocked her into cover.
Leon told Sherry that they would provide her and Jake cover to a nearby exit. Sherry agreed, and they executed the plan, Sherry and Jake making a run for the doorway. Once there, a J'avo caught them off guard and Sherry pleaded for Jake to run. With a smug look on his face, he refused, and Sherry replied, saying he'd promised. Revealing that he'd lied, the two tried to fight off the growing masses of J'avo until they were finally overpowered, disarmed, and taken to an underwater base.
"There are more important things at stake than you and me."
— Jake to Chris
When Sherry and Jake woke up, they found themselves bound up. Sherry apologized to Jake for trusting Simmons and not seeing through his lies. Suddenly, they were somehow set free and Sherry rushed through the air vent to get their weapons and get Jake out of the cell. Fighting their way past a horde of Rasklapanje, they activated an elevator, but barely escaped alive when one of the creatures caused the facility to overload and spiral out of control.
As they made their escape, they encountered Chris and Piers, who were the ones that freed Sherry and Jake. When Chris revealed that he killed Albert Wesker, Sherry and Piers tried to stop Jake from shooting him out of anger. Jake didn't kill Chris, knowing that there were more important things at stake, but their conversation was interrupted when HAOS began to awaken, so they take the lifts up to the top. Once they reach the top, they witness Haos emerging from its cocoon. Dodging its attack, Sherry and Jake make their escape while Chris and Piers stayed behind to defeat it. Sherry wanted to go back and help, but Jake told her that it was their choice to stay. After being reminded that they had to save the world, Sherry hurried with Jake to the exit.
Entering a room filled with hot lava, Sherry and Jake are confronted by Ustanak once again. In the middle of the fight, Jake and Sherry are separated by Ustanak and Jake is trapped with it on an isolated gantry section. Without a weapon, Jake decides to face the creature with his hand-to-hand combat. After a series of well timed attacks on Ustanak, Jake lands the finishing blow on the monster and sends it falling into the lava. As the facility began to crumble, Sherry and Jake made their way to the exit. They found a lift that traveled at a fast speed, but they were met with Ustanak and a gush of lava. Trying to fight him off, Sherry spotted a gun and quickly grabbed it, pointing it at the monster. But she had a hard time keeping her hand steady, so Jake helped her in firing and killing Ustanak once and for all. As they held on for their lives on the lift, Jake thanked Sherry for saving his life.
"Fair's fair, kid."
— Jake to the boy he helped
After the life-altering experience Jake had went through, he decided to make a change in his life. When he and Sherry parted ways, he sent her a message through her phone to inform her that he had lowered his asking price - from 50 million dollars to 50 dollars. Looking out his window, the boy watched as numerous Napad dropped from the rooftops around the small building he was in. Stepping back from the window, the boy bumps into a hooded Jake Muller who asked the boy if he had what was asked for. Still surprised, the boy hesitated momentarily before taking out an apple and handing it to Jake. As Jake left through the front door, the boy asked him if he would keep his promise. Jake whipped off the cloak and hood as the Napad began to charge him. Drawing his pistol, Jake took a bite of the apple and told the boy that, "Fair's fair," then proceeded to open fire on the attacking B.O.W.s. This shows while Jake is more interested in helping people, he still maintains a mercenary image.