After a bit of playing around, the portal was figured out - one location seemed to lead to the edge of the universe, and another... to Earth.
The plan was thus:
First, as quickly as possible, the portal would be opened, and as many ships as possible would move through the portal, to the edge of everywhere. The enemy ships would follow, then the civilian ships would circle back, leaving the Hephaestus behind to Jump. The rest of the ships would travel via the portal to Earth, and meet up with the Hephaestus.
It was an all-out battle. The Silver Surfer, the Hephaestus, Galactus, Elise's Stormfalcon, Rodney's Punch Ship, as well as an army of other ships fought the swarms of deader ships that arrived minutes before the last ship cleared the portal. Reggie, having damaged his main gun, lead the other through the portal; as it turned out, though, their tactics saved the day, and Rodney's ship tore through the enemy ships with ease. Still, the Forgotten ships were formidable, and one managed to break through their lines, heading for the portal. It went through; the other ships quickly zipped in behind it, leaving it behind with no targets. Before it could turn, the portal was closed, and it was cut off from everyone, forever. Reggie, meanwhile, lead the other ships through to Earth.
The few remaining ships saw a strange, wobbling, silver blob appear... and suddenly split apart, releasing clouds of gas. Or... not gas, but nanites! Chrome, still aboard the Haephestus, saw the gray blob, and recoiled. "I've not seen that in thousands of years... but I'd know that shape anyway. Those are the destructive nanites that gave me life - and killed so many!"
The nanites made straight for the ships; any attempts to shoot them do nothing. They were too hard to hit, and much too tough to just burn with laser fire. The nanites split into pieces, and as they approach the ships... vanished. Then reappeared inside.
Rodney tried ramming them, but found they teleported into his ship; a face suddenly appeared, then just as suddenly vanished. A whisper in his comms scratched out, "Survive..."
Elise saw the same thing - a shifting form of life, a humanoid figure full of smoke and nothingness. Her comms picked up a simple, short-range signal that sounded like a scratchy recorded message. "Hear this, and tremble: we tear down gods to avenge our own. We have become Death, destroyer of worlds." With that, the nanite swarm gusts through her ship; all her beautiful robots suddenly glitched, shuddered, and fell silent as the swarm of nanites ripped through the ship.
Nix, on the Hephaestus, also saw the shifting form appear - but Chrome make a sudden decision. Grabbing Silver, he threw her towards the swarm, then leaped after her. The nanites, interrupted, began attacking her, and Chrome; the scratchy recording played, gradually getting fainter, as Silver twisted and shuddered. Chrome, too, was attacked; every time it seemed Silver was about to be overcome, however, Chrome seemed to somehow help her. Before anyone could react, the nanites swarmed Chrome and Silver. Chrome screamed a metallic roar, and dropped to one knee - or, rather, fell because his leg had been eaten entirely away. Silver writhed, her skin dancing like ripples in a pond, until suddenly, Chrome fell into a puddle of silver goo, and Silver... changed. Her form still had a feminine shape, but it was wildly different from how it used to be. Now, she looked like a cross between a frog and a turtle. She seemed to still be functioning, however, holding her hands to her face, staring into nowhere.
With the nanites gone, Silver seemed confused and lost. Luckily, she could still remember how to translate the coordinates to set the portal, and eventually dialed in Earth. She had a few faint "memories" from the nanites, and has held on to much of her past life, though most of her special abilities.
The Earth that remains is, well... it's not in good shape. In fact... it's desolate. No human being remains. The good news is that the crew still have the resources of the planets left behind; with the portal operational and the nanites and Forgotten gone, the stations, moons, and planets can be sourced for materials to rebuild Earth.
But what actually happened? Why is the Earth dead? Well, travel can be a tricky thing. According to the Hephaestus, the old galaxial maps should fairly easily match the stars. It took a little while, but it seems as they've arrived around thousands of years after they left!
A single signal blinks on from the Earth - "Earth has been located. Further orders required. Earth has been located. Further orders required..."
A group of robots, hidden in an underground bunker, give their last message: their planet had fallen, and they came to Earth to tell them, but found only destruction. They've been here for hundreds of years, waiting to relay their final message. "As far as we can tell, Earth was abandoned 2000 years ago..."
Reggie formed a mafia alliance, becomes significantly more powerful, and raises funds by selling museum tickets. Elise began repairs on, well, everything; she's set in charge of the portal, and commences detailed study of it.
The planets left behind are not all in bad shape; the people set up a federation, to assist with border disputes. For now, everyone needs to work together to rebuild Earth.
Rodney, meanwhile, doesn't want a lot - only requires a handful of things, really. He wants a military title of "Rodney"; three suits of power armor (one for Rodney, one for Lins, and one for his chicken), and his ship to be rebuilt; and wants to rule over Texas and northern Mexico. He finds a couple rounded rocks, punches holes through them, and gathers his crew. "Captain, show Lins the ancient Earth custom of marriage."
Reggie wants to commission an "In Honor Of" statue for Chrome - without him, Silver would still be an weird non-sentient construct. He doesn't need a country; he just floats around in his, er, mafia space museum.
Elise, of course, sets up production, churning out robots and equipment; Nix works overtime to jumpstart the government.
Hoping to discover what became of humanity, they send out exploration missions...
And then, a small, boxy ship comes out of Jumpspace. "Who are you? And what happened to Earth?"