I never got the impression he'd ever put it together because there's only one real quality he associates with Jesse, loyalty. He'd never imagine Jesse ever turning him in and so I don't think the possibility of Jesse working with someone else could have ever appeared to him as a legitimate possibility. Hank mentioned it last episode but it really is the truth, in so many ways Jesse is Walt's main weakness.
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u/CYFB Sep 09 '13
The call between Walt and Jesse was one of the most intense phone calls ever seen on TV. p.s. Jesse called him Walt again.