Summary of Grovyle's version of the story:
The planet's paralysis started in the past (your time), when the Temporal Tower, Dialga's domain, collapsed. With the collapse of the Temporal Tower, the time went out of whack and eventually stopped. Dialga, whose fate is tied with the Temporal Tower, also lost most of his reasoning. Now, he is a mere shadow of his former self - a being that feels no emotion, outside of his own self preservation. Thus, he seeks to prevent the history from changing. That's why Grovyle and Dialga is at odds, because Grovyle wants to set right what once went wrong. Dusknoir is an agent of the new Primal Dialga, sent to the past (your present) to stop Grovyle. Grovyle was taking the time gears only because he needs to put them in the Temporal Tower, to fix the ROOT of the problem. It's his badass attitude that misguided people. Grovyle will go back to the past again - with the help of Celebi.
Your partner found it REALLY hard to believe that Dusknoir is a villain, and struggles with himself. Grovyle apparently has no interest in helping him sort out his emotions, but you will eventually have decided to trust Grovyle and follow him.
Meanwhile, you get to see Dusknoir and Primal Dialga again. Apparently, the stage is set and now the main players (you) just have to walk in, and they will capture you! We'll see about that.
Now, you re in front of another dungeon. You may recognize this place as the future of your base camp back at the expedition, so I guess Dusk Forest here is the future version of Foggy Forest. Anyways, save, prepare, whatever, then enter.
Dungeon - Dusk Forest[edit]
Lol, a dungeon with 4 types of Pokémon. Anyways, for the dungeon you will have the help of Grovyle who is level 46(!), with a moveset of Absorb, Quick Attack, Leaf Blade, Dig. He kind of lacks range, but unlike Bidoof (or those pesky escorts...) he can take out all sort of crap by himself, and is not running danger of being KO'd any time soon. A great ally to have around indeed - if he is behind you instead of your partner and you run into trouble, displace him and let 'im fly. Anyways, the dungeon doesn't have foggy weather like Foggy Forest, so your electric moves are safe. The residents here don't hit too hard so you're pretty safe, though Mismagius being a ghost type can travel through walls. Jumpluff can hit with STAB bullet seed, so watch out for that too. The dungeon is rather short, and with Grovyle around you're not going to have a hard time killing things.
At the end of the dungeon, you will meet Celebi herself. She is quite a funny gal, and provides some much needed comic relief in the series of events, so I won't spoil the scene. Anyways, our next destination is to march on, so Celebi can teleport us back to the past. Celebi seems to know something weird about you that nobody else realizes, though... but she shrugs it off. So, yeah. Prepare, save, whatever. Oh and, make sure you talk to Celebi before you enter the dungeon!
Dungeon - Deep Dusk Forest[edit]
Wow. As if travelling with a level 46 Grovyle is not easy enough, we now have an ADDITIONAL level 45 Celebi. Celebi can use Magical Leaf and Ancientpower to attack, Heal Bell to cure status for the entire team, and Recover to, well, recover her own HP (not that she needs to, but hey...). Given that Magical Leaf is ranged and hit half the dungeon for super effective damage... As for the residents, Rhydon can hit you with STAB Rock Blast and... that's about it. Nothing hard here, though Hippowdon has Sand Stream and can be annoying. But if you have a Grass Type partner (or you as a Grass Type Pokémon), you can beat anything in this dungeon.
At the top of the forest, you see the passage of time. But then, Dusknoir shows up in front you to block your progress. Looks like there's no other choice... we must fight! Oh wait, Dialga is here too. Crap. We're screwed now. But hope is still alive, or so says Grovyle - for a human travelled with him the first time he went in the past! There was an accident that separated the human and Grovyle, but the human must still be in the past, working diligently to stop the planet's paralysis. Who is that human, you (or rather, Dusknoir) asks? It is none other than [your starter's name]!
But you're right here! Dusknoir steps in now. He knew for a long time that you was Grovyle's partner, and though he does not know how you came to be, your amnesia made it quite easy for Dusknoir to manipulate you. So, this is the grand plan for Dusknoir - to trash your hope in the end. Despair doesn't get much better than this.
Your partner isn't about to give up, though - Celebi, take us and travel even for a short while in time! Never mind that Dialga is here and will laugh at any puny attempt to mess with time (the passage of time is not puny so Dialga can't laugh at it), it's enough for you to get an opening and get in the passage. Good job, partner.