One of the advantages of 24's format is that it presents a unique opportunity to examine relationships at different stages. In season two, we see Tony and Michelle as coworkers, maybe friends. By the time season three begins, they're married. This allows viewers to compare their relationship over the course of two similar disaster scenarios and several different conflicts that present within each season.
1. The Beginning
Tony and Michelle start off with a friendly relationship, and there's a vague indication that they may be attracted to each other. At the very least, they work well together and seem to respect each other. Heeding advice given by CTU director George Mason, Michelle hits on Tony in a brief moment of calmness. It's pretty cute. There's obviously potential there.
2. Proving That A Working Relationship Just Isn't Enough
The second half of the season shows that this foundation isn't strong enough to withstand a difference of opinion regarding an international crisis. A couple of greedy oil executives try and pin the day's nuclear threat on three countries in the Middle East (see track #10), and the US government is about to launch an attack against these countries. Michelle thinks the three countries had no part in the day's events. Tony disagrees. So Michelle spends the next few hours helping Jack Bauer prevent World War III behind Tony's back. Honestly, Tony's skeptical position is understandable; however, it's a significant difference of opinion, and it shows that Tony doesn't exactly respect and trust Michelle in a more complicated situation.
3. United by A Shared Goal
Once the evidence wins Tony over, he and Michelle defy the powers that be and do what they can to help Jack Bauer save the day. When Ryan Chappelle, the director of Division (a superior government agency), insists they stop helping Jack Bauer, Tony and Michelle work in cahoots to subvert Chappelle's authority. For the most part, they seem to be united by their desire to do the right thing and prevent the world from nuclear annihilation, but the sexy emotional breakdown kiss they share in a dark hallway indicates that they may still attracted to each other, so there's hope for the future.