Subaru and War-Rock make their way to Meteor G, where they take down Jack and Queentia, and talk them out of working for Meteor G. Virgo and Corvus are displeased, to say the least, and try to kill Jack and Queentia, but Solo intervenes, takes out Corvus/Virgo, and gets Jack and Queentia out of there. Subaru and Rock continue on.
At the meteor's core, they find Daigo, who (presumably) was able to work his way there due to being an EM form. Before they can destroy the core, though, King reappears and fuses with the core, creating Crimson Dragon. CD... eats, for lack of a better word, Daigo, and you fight him as the final boss. King goes boom. CD does not. Subaru gets knocked out.
After a brief interlude in the white-space-of-consciousness (TM), Shidou appears and helps Subaru out. Subaru turns into either Red Joker or Black Ace, and you fight a rigged version of CD (he has 8000 health, but you have ridiculously good cards and can't die.) CD goes boom. Meteor G goes boom, with Daigo, Subaru, and Rock still inside it. Oops.
Subaru ends up floating in space as EM waves. Daigo manages to get ahold of WAXA, where everyone else is gathered, and delivers the bad news. Akane is less than pleased by her MIA husband telling her that he's still MIA and now her son is too. The head of WAXA, this old woman whose name I can never remember, proposes using everyone's Hunter VGs to send out a signal to pull in Subaru. Cue obligatory everyone-around-the-world-gives-their-support montage.
Subaru wakes up in space, with Daigo and Rock there with him. But they can't come along for the ride, and Subaru gets pulled back to earth, while they stay lost in space. Over the credits, we see Subaru having a celebration with Misora, Luna, Gonta, Kizamaro, and Jack, Solo and Laplace standing someplace being mysterious, Queentia, Acid, and aforementioned old lady taking care of Shidou in the hospital, and Subaru looking up at the sky.
After the credits, Subaru's on the roof of the school, looking up. Suddenly, an EM meteor appears and lands in front of him. It's Rock! The two hug, but the celebrations aren't over yet, because true to Capcom's no-good-people-ever-die rule, Daigo also shows up. The three return home, and Daigo and Akane have a happy reunion. Cut to ending picture of Daigo giving Subaru, Akane, and Rock a group hug (which you can see in someone's album here.)