Wesker continued to be flooded with questions regarding Spencer's true motivations regarding B.O.W's. In 2006, he discovered the whereabouts of Spencer and traveled there to find answers. Wesker expected Spencer to be surprised by his arrival, but much to his shock, the old man seemed to actually expect Wesker to arrive. It was then Wesker realized that Spencer had been in control of everything from the start, including Wesker's own actions. Spencer revealed that the development of B.O.W's was only a part of achieving his goal of forcing human evolution through viruses. With the birth of a superior human race, Spencer would make himself a god. Spencer required three things to accomplish his dream: the progenitor virus as a primary viral base, the Umbrella Corporation for funds, and people who would share his ideals when an advanced race came to be. Much to the surprise of Wesker, Spencer revealed Wesker to be the result of the third necessity.
In a plan called the Wesker plan, Spencer collected hundreds of children from parents of superior intellect throughout the world. These children were all given the surname Wesker, and Spencer used indoctrination and manipulation to install his values into these children. They were then put in controlled environments all over the world under Umbrella's watchful eye. These unaware children would continue to live their lives and received advanced education with the help of Umbrella. One of these children was eventually sent to Umbrella's training facility. That child was Albert Wesker. Spencer then gave all the Wesker children an experimental virus, Albert's being received through Birkin. Only a few of these children survived, including Albert. The surviving children were then programmed to seek Spencer out. Unfortunately, now that the truth was revealed, the only thing impeding Wesker was an old dying man. Wesker killed Spencer by thrusting his arm through his chest, claiming the right to be a god to now be his.
Just then, Chris and Jill entered Spencer's hiding place only to find Wesker there. Stronger than the two of them combined, Wesker sought his revenge on Chris once and for all. However, before he could deal the finishing blow, Jill sacrificed herself by pushing him out of the window, causing the two of them to fall into the chasm below.
The B.S.A.A. searched for the bodies, but were never recovered and the two were marked as deceased. In fact, the two survived and Jill was captured.