Walt Jr. came up with the nickname Flynn when he was sick of all the lies his dad was telling. Since then, referring to Junior as Flynn has been an indicator that that person is not pleased with Walt. In the last episode, Marie called him Flynn because she didn’t want to associate him with his murderer father. However, Skyler called him Walt Jr. because she was still loyal to Walt to some degree. Now it is clear that no one wants anything to do with Walt and Junior has gone as far as to make sure no one ever calls him Walt Jr. again.
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