Resident Evil 4
In any game Wesker's been in, as in physically showed up in, he's mostly behind the scenes in Resident Evil 4. His role in this game isn't complex, but at the same time, is highly shrouded in mystery. With six years having past since the last time we saw him, lots has changed apparently, and nothing is really given to explain how he's in the position he's in. But it's very clear what he's after, so here goes.
Warning: Spoilers!
Ashley Graham, the daughter of the President of the United States, has disappeared in Spain. Leon S. Kennedy is dispatched to investigate the matter, find her, and bring her home. But what he hopes is going to be a simple missions turns into the second fight of and for his life.
Ashley is being held against her will by a cult group infected by a parasite and controlled by their leader, a man named Osmund Saddler. During his struggles, Leon runs into an old, and familiar face, Ada Wong, who is there for mysterious reasons she never really reveals. But it seems to be true during their first meeting that she is, in fact, working for Wesker.
In the side game, Separate Ways, in which we control Ada Wong, we find out that she was dispatched by Wesker himself, as he only actually appears in this minigame, and that he dispatched her to aid the first agent he'd sent in, Jack Krauser, in obtaining a sample of the parasite infecting the villagers.
Wesker is the one who usually sends Ada on her missions which we play through during the game. He first tells her to ring the church bell to get the villagers to quiet down so that the mission will be easier for Ada, and shortly following, he instructs Ada to rescue a planted researcher, Luis Sera, who is set up to give Ada the sample in return for extracting him from the village.
Shortly following these events, Wesker contacts Ada and tells her to kill Leon Kennedy at any chance she gets, but when opportunity 'doesn't present itself', or more so, when Ada claims it hasn't presented itself, he changes his mind and decides to capitalize on Leon's 'lucky streak'. If Leon can cause enough of a distraction, Ada will be able to get the sample from Saddler more easily.
As time goes on, however, Wesker apparently no longer wishes to hold to this strategy, and informs Ada that Krauser has been sent to 'take care' of Leon, and that she is to get the sample at all costs. Ada disobeys Wesker, however, and goes after Leon to save his life, succeeding, and making a true enemy of Krauser in the process, who is completely loyal to Wesker.
Not long after, Ada reports Krauser as having been killed at the hands of Leon, and with no other choice, Wesker says to let Leon and Saddler duke it out. Ada's only remaining job is to be sure to clean up what's left of them after the fight is through. The only thing that matters is the sample, and nothing will stand in their way, or more specifically, in Weskers, or his companies.
After these events, we don't see or hear anymore from Wesker, but we are given a report by Ada that states she'd sent Wesker a gift besides the specimen. So now we know for a fact that Wesker has been betrayed by Ada, and has some type of fake Las Plagas sample in his possession. We also know that Wesker has significantly risen in his social status in Umbrella to what many believe is the owner itself. Though his dress is typical of some kind of spy or assassin as well as a well-to-do individual, so it is possible that he's still an agent within Umbrella's stronghold.
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