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I have the feeling that Jack is not really Syndey's father and instead her entire childhood was a lie/false memory as her being part of Operation Christmas. Syndey is a government test (think "Dark Angel") and had even less control over her life than she originally thought.
Re your: 2. I'd love Irina to be the man too, but unfortunately, unless they recast the role (Lena Olin supposedly has no intention to EVER return) I can't see that being a huge story line.
Re your: 3. Of course Lauren isn't dead!!! No one ever dies on Alias!
Re your: 5. I thought S3 explained that Sydney was working with CIA for a good portion of the two years she was gone.
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