Why and how did the humans capture Supergirl

So the lovely sexy Supergirl reveals that she came in a pod with superman to earth. I didn't quite catch if Zod was tracking them and followed or came with them.

Either way he's looking for her and the humans have imprisoned her in Siberia in some underground bunker? Why would they do that? They seem to be scientists but is the implication that they're studying her to see how to defeat Zod (but looks like he is not here yet? And so they don't know Kara and Zod are from krypton). Also how would they even have captured her?
The whole back story here was not needed for The Flash understandably but it would be good to explore.

So Kara either came as a kid or some good amount of time earlier given her statement ("it used to not be so loud") on the manor terrace with Barry. It also implies she was imprisoned and studied for a while.

So she should be at max power or now a friend of Earth which clearly wasnt the case.

This means only one thing : they know about and have kryptonite. Ergo, they should also be able to defeat Zod easily. They could have either drained her to normal human using kryptonite or killed her etc. But probably studying her drawing blood.

With Zod however they face extinction so they could have used Kara's help with kryptonite to render Zod and his peeps useless super easily.

Barry wouldn't need to really save his universe because if smartly done no one superhero would have been killed.

Anyways I sorta liked the movie. Would have preferred the TV actor who is a lot more effective as Flash but this guy was OK I guess.