Why Did Ada Wong Work for Wesker?

Ada Wong worked with Albert Wesker because they had the same employer. Both were agents of a company competing with Umbrella, and Wesker, a former Umbrella insider, was her contact on its most important jobs: the G-Virus in Raccoon City and the Las Plagas parasite in Spain. She was never really his. By the end of Resident Evil 4 she says outright that she was only pretending to work with him. (Resident Evil: The Umbrella Chronicles; Resident Evil 4 (2005))

Same company, different agendas#

In the original Resident Evil 2, Ada is a spy after the G-Virus for an unnamed company, and Wesker doesn't appear in her story at all. The link came later. The Umbrella Chronicles, which retells the series' early years, shows that Wesker was running the Raccoon City operation for the same company, watching Ada's progress and stepping in to get her out when the city fell. (Resident Evil 2 (1998); Resident Evil: The Umbrella Chronicles)

The same game's file on Ada explains how they came to be paired. The company didn't trust her at first: she wouldn't say who she really was, and her loyalty was hard to judge. Wesker vouched for her, and that endorsement is what got her the work. From then on he was the person who handed her assignments. (Resident Evil: The Umbrella Chronicles)

That's the plain answer to the question. Ada is a professional spy, and Wesker was the senior agent her employer put between her and the job. She took his calls because that was the contract. (Resident Evil: The Umbrella Chronicles; Resident Evil 4 (2005))

A working relationship, not loyalty#

They also worked against each other. In 2002 Ada approached Javier Hidalgo, a South American drug lord buying Umbrella bioweapons, offering her company's products instead. Wesker's faxed messages in the Darkside Chronicles have him warning Hidalgo that she was an Umbrella spy. (Resident Evil: The Darkside Chronicles; Resident Evil: The Umbrella Chronicles)

Spain in 2004 is where the gap shows. Ada was sent to get a sample of the dominant Plaga from the cult Los Iluminados, with Wesker giving the orders and Jack Krauser working for him too. When Leon kept getting in the way, Wesker ordered Ada to kill him. She didn't, and she saved Leon several times instead. (Resident Evil 4 (2005))

At the end she took the sample from Leon at gunpoint and escaped. Then she double-crossed Wesker. Her report at the end of Separate Ways says she sent Wesker "a different present, just as the organization ordered", keeping the real sample for her employer. (Resident Evil 4 (2005))

Why she turned on him#

The reason is in her reports. The company believed Wesker was working for himself. Ada writes that Umbrella had been a shield for his own plans, that he would try to build a new one now it was gone, and that he had been in contact with a giant pharmaceutical firm, which she calls only "S", since Umbrella's fall. By Resident Evil 5 Wesker's partner is the drug company Tricell. (Resident Evil 4 (2005); Resident Evil: The Umbrella Chronicles; Resident Evil 5)

She also writes that Wesker knew exactly what the company was thinking, and that the two of them were playing cat and mouse. So she wasn't fooling him, quite. Both of them knew the other was holding something back. (Resident Evil 4 (2005))

The 2023 remake of Resident Evil 4 and its Separate Ways chapter keep the same outline, with Ada taking Wesker's orders in Spain and keeping her own counsel, though the scenes play out differently. (Resident Evil 4 (2023))

After Spain#

That's effectively the end of it. After 2004 Ada takes jobs from other clients, including Derek Simmons, whose obsession with her leads to the C-Virus double Carla Radames in Resident Evil 6. Wesker goes his own way with Tricell. (Resident Evil 6; Resident Evil 4 (2005))

Our reading, and it's only a reading: Ada never worked for anyone in the sense of belonging to them. Wesker was useful to her, she was useful to him, and when the company's interests and his split, she sided with whoever was paying, and with Leon. More on her side of the story is on Ada's page, Wesker's is on his page, and Spain is covered in full in the Resident Evil 4 story. (Resident Evil 4 (2005); Resident Evil 6)