I have been wondering the same thing. Irena dissapears at the end right before she tells Sydney "Your the chosen one not me." and jumps off a skyscrapper.
I don't know if I am the only one to think this but, if Irena knew that Sydney was in fact the chosen one, why would she dissapear, leaving Sydney with unawnsered questions, and what exact rolls did she play to gain that information and act on it? *May sound confusing, sorry*
When Irena relays this information to Sydney, disapears, adn then Sydney disapears, it makes me think that Irena is a prime suspect in Sydney's disapearance.
Any other suggestions?