Sim gives a very good explanation in the first post.
I thought/think Grovyle's pretty awesome. At first, I was rather disappointed, seeing that how one of my fav Pokemon (Treecko is one of my all-time faves, so yeah... its evolutions are also) was the antagonist of the game.
However, it was rather awkward how when Dusknoir left... you're pretty much fully persuaded that he's a protagonist, but when he dragged me into the portal like he did, my mind was filled with confusion. Eventually I had started a conclusion that Dusknoir was the antagonist after I had came to the scene with the two main characters in the jail cell. It was just... well, different, yet amazing how the programmer(s) of the game make your opinion shift just like that.
I was confused even more after Grovyle was helping the two main characters escape the future and such... at first you'd think it would be a trap, but shortly after you come to understand everything. I did find it annoying, though, how the partner character kept on doubting Grovyle like there was no tomorrow. I know that the partner character has a cautious personality and such, but still. It almost made me conclude that Chimchar (my partner character)'s doubting would greatly interfere with the story sooner or later. However, eventually he shook that feeling off, which is great.
But as soon as you return to the past, things are made much more clear... I mean, at the beginning of the game, you learn that the thief, Grovyle, is stealing the time gears, and that if all of the time gears are misplaced, then the world's paralysis will come to be. However, once all of the time gears are replaced, you become confused to see the world's future to be in total paralysis.
Once Grovyle explained the whole deal about how the time gears needed to be placed in the rapidly collapsing Temporal Tower, you slightly start to understand. However, once he clarified that taking the Time Gears out of their place didn't permanetely stop time, instead temporarily stop it within that area, things were fully clear to me.
However, I was a bit shocked to hear that the main character and Grovyle originated as best friends, obviously knowing each other for quite a long time....
But once you have beated the main storyline... you only know half of the reasoning. In the post storyline, you learn that the whole cause was Darkrai's fault; for he was the one who wanted to rule a world of complete darkness, and how he was the one controlling Dialga.
I forgot to mention how much I loved the ending of the main story... I actually found the disappearing of the main character to be the most saddening part. I mean, seriously, your partner is completely clueless of this secret, for you must hide it. Once you start to vanish, the partner character is in a state of confusion and shock.
And the music... it just sets the tone even more.
Seeing how emotional I can be, I kinda started crying before long....
Oh, yeah, and I ALSO forgot to mention that the Primal Dialga/Dialga fight music is oone of my favorite themes in any Pokemon game. It's amazing.
Overall, I enjoyed the entire storyline more than any other Pokemon game... it was extremely well-though out, it seems; in fact, just saying that would most likely be a complete understatement.
I liked it so much better than I did the one for the first MD game. I mean, seriously, there's a large gap of improvement between the two.
And Celebi's personality was so... kawaii! X3 I thought it was so cute how it seemed so much that she liked Grovyle. X3
It still remains a mystery to me, though, how she was shiny. :\