The first season of Nikita had two sides--Nikita and Alex on one, and Division on the other. Their roles were clearly defined and it was already evident what they wanted. In the second season, things are much different. There's still the story of Nikita vs. Division, with Michael and Birkhoff joining Nikita's side and Alex leaving, but there is also the increasing reach of Ari Tasarov and Gogol, and Sergei Semak and Zetrov. There are so many competing interests and secrets that every plot gets tangled in a web of lies.
"Partners" shows us the fleeting bonds of partnership, as Nikita's former partner could only be loyal for so long before helping Gogol. While Nikita may have saved Alex this time and will continue to do so, Alex is deadset in her objectives and is a threat despite Nikita's goodwill.