Drake is with the secret organizasion called Section 31, which works outsied the "law" if you can say it that way.
I did this mission both on OB and in live and have tried both sides.
Thing with this mission is that its not the last you have seen of drake.
I havent seen him again after that mission, but what he says before he leaves makes it clear that you havent seen the last of him.
I suspect he will come back again at some point in future content.
I sided with drake, because carna said that drake was a member of section 31. How the hell did he know that?
Not to mention that if an Undine had successfully impersonated a Section 31 agent, why was he wasting time messing with a single ship when he could be destabilizing Alpha Quadrant further by airing all of the Federation's dirty laundry, killing their best covert agents, and/or using all their information? Of the choices presented, siding with Drake was the logical one.