Day 4: 12:00 A.M.-1:00 A.M. - S4-E18
Continuity mistake: To get crucial information from Prado, Jack offers his resignation to Buchanan, and takes Prado on as a private citizen. But Jack doesn't work for CTU; he works for DOD, and is at CTU on a provisional basis.
Answer: According to Jack in season 5, Nina was "deep cover" before the pair ever met, so it's safe to assume she was recruited before she joined CTU. As for what her primary mission was, who knows? Perhaps it was to gather sensitive intel and pass it on to her superiors. Given that she worked for an intelligence agency, it's not a stretch. Or perhaps we may find out in season seven.
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