I'll be honest
You don't have to listen to anything I say in this review, but try to take some of it into consideration as you continue this series. You appear to have the passion to want to make the series, but remember you are making it for other people to watch too, so it might be your vision but try to have the viewer in mind when making something. Also, I am not attacking you at all in this review, just trying to help out and give suggestions.
So lets start with what you did well. You can draw pretty well and had some nice details present. Your movie did have a direction to it and always had somewhere to go. Your movie is better than most of the stuff here on Newgrounds.
You came up with a very overused story which means you have to do an excellent job to override the fact the plot is cliche(which you didn't do). The animation/art of this animation looked a lot like a poorly done Esurance commercial (the main character reassembled the girl in those commercials a lot). You really have to work on your animation, and add some fbf in there to make it look much more natural since nearly all of the movements were too clunky and robotic. Now, I don't really have a problem with art as a standalone thing, but it was that the style really didn't match the theme/plot at all.
That is more a matter of direction. The story plot from your movie i assume is dark, and the art (for me) came off as overwhelmingly happy. I couldn't feel for the character. It just didn't go together. I didn't like the limited animation at the beginning that relied too much on your character design and voice acting.
The color scheme didn't really change too much once on the spaceship thing. You played with lighting a tiny bit, but it still wasn't scary, and didn't pull me in. The camera was also too jerky. Also the bitmap images you used felt extremely out of place.
The entire movie moved too fast. I didn't believe anything, there was no suspense, or tension throughout the entire thing, so it wasn't engaging for me the viewer at all. You didn't build the aliens or any of the events it all just kept happening, and because of that, it because rather boring. I didn't feel lost at any point either, so I wasn't feeling for the girl character in it.
I didn't really enjoy the dialogs at the beginning. It felt like a script was being read, it just wasn't natural. The voice acting was interesting at all either.
So you are trying to achieve a vagueness in the first episode to make people interested and watch again later right? It really didn't work for me like that, you had no real exciting things happen that made me interested. It was all just there. I felt no real mystery or thrill aspect to it. That style isn't new, it's not different, it's done all the time, and it's bad, it's amateur. Nice try though, we all have to start somewhere. Even the stuff that people assume is the "doesn't revile a lot at a time" plots like Lost or Heroes still has interesting characters that pull the viewer in. Whatever.
Aside from all that, people seem to be enjoying it. I'll be sure to watch your next episode.