Alternate Ending 1: Vegito
Prime burst out of the moon's surface where he had hidden himself, finally completely remerging with the universe and synching back with the time stream by force of will. He wrapped his arms around the super saiyan's chest. His suit was ripped to shreds and half of his face was still ragged, but he still lived, beyond all expectations. And now he would get his revenge.
"You thought you could kill me? ME? I don't die. I survive. I ALWAYS survive!" Prime screamed insanely. "And now I'm going to squeeze you to a pulp."
Goku felt Prime's massive strength squeezing against his body. Superman Prime had clearly lost a lot of his power, though once again back in the sun's rays it was starting to build again. Part of why Goku had not been able to detect Prime's ki energy was that it had partially been in another universe. The other reason was that, weakened as he was, the power level was not as apparent to Goku as it had been before. At the moment, Prime was only about as powerful as Superman. But in Goku's fatigued condition, the saiyan knew Prime's strength would be enough to crush his body.
"Darn!" Goku called out. "I thought I destroyed you." The saiyan glanced over at Superman as he struggled to resist Prime's crushing strength. "You had better get out of here, Kal-El."
Prime's grin was wide and evil. "I'm the real Kal-El, but that imitation should take your advice. Because after I kill you… he's next!"
Superman Prime squeezed.
BLAM!
A blast to the back of Prime's head caused him to open his arms up wide, allowing Goku to dematerialize and reappear away from the crushing grip of the Kryptonian. Goku turned around to see who his benefactor was when he heard the callous sneer of a very familiar presence.
"Nobody kills Kakkarot but me."
Vegeta stood floating in the air, his arms crossed in front of him with his typical proud, arrogant smirk on his face. "So, this is the powerful Kal-El that impressed Kakkarot so much. Now let's see how you deal with a REAL super saiyan!"
Vegeta blitzed Superman Prime with a burst of speed, landing hundreds and thousands of blows on the startled Kryptonian before he could register the attack. Vegeta had worked himself constantly to train to catch up to Goku, his long time rival. They were friends of a sort, even family in some ways, but Vegeta never lost sight of Goku being the one person he must defeat, he must surpass. This for him, was an opportunity.
And he was doing it. He had reached the level of Super Saiyan 3, his sharp golden hair stretching down all the way all his back, his aura of power flashing and crackling with unrestrained power. His opponent was being smashed before him. The guy could take a pounding, that was the one thing going for him, but Vegeta continued to pour on the beating, moving around the defenseless enemy smashing him with a fist to the face, an axe-kick to the back, a chop to the throat. The fool Kryptonian couldn't even manage to block a single attack! And his rival, who moments before had been held helpless by this weakling, was left there to do nothing but cheer him on.
With a final planet-shattering fist to Superman Prime's back, Vegeta sent the Kryptonian plummeting to the moon. A brand new crater the size of a city appeared on the Earth's natural satellite where Prime hit the surface. Vegeta stood there in space, his chest heaving. "And that's why I'm the Prince of all Saiyans!"
"Vegeta! Finish him! Don't give him time to recover!" Goku warned.
Odd that Kakkarot would advocate finishing an opponent off. Vegeta looked at his rival with a gloating expression. "What? All out of mercy, Kakkarot? And I thought you would be the first to want to give someone a sporting chance. I guess losing like you just did to that overgrown fool must have hurt your pride," Vegeta laughed. "About time. But I can do this all day!"
"Not that I don't mind the help, Vegeta," Goku mused. "But how did you get here and how are you… you know, breathing in space."
Vegeta smirked. "Oh, did you forget already? When I ascended to the level of super saiyan I was training out in an asteroid field without any kind of protective suit. Elite saiyans learn to regulate their breathing on such a level that we can go extended periods in the vacuum of space without air or needing any kind of protection. But of course, a low-class saiyan like yourself wouldn't understand that, now would you."
"Well, it's great that you're here, and thanks for your help, but why again did you come?"
"If you must know, I was sent here by King Kai to bring the Dragonballs to this universe so that you can wish back all the people you killed while you were being a weak-minded idiot. Now that I've taken care of that—"
Vegeta never finished his sentence. A powerful fist from Superman Prime connected to Vegeta's gut. The Prince of Saiyan's eyes bulged out of their sockets and the super saiyan spit blood.
"TAKEN CARE OF ME? I'M SUPERMAN! NOBODY TAKES CARE OF ME, I TAKE CARE OF EVERYONE!"
"You mean, like, you take care everyone by looking out for them and making sure we are all okay? That's really thoughtful of you..." Goku asked innocently.
"No! No, no no!" Prime screamed. "I take care of everyone, by KILLING THEM!"
Vegeta was fortunate that Prime had taken the time to shout his nonsense and bothered to respond to Goku's jibe before attacking him again. Only after taking a direct hit did it register what kind of enemy he was facing. Despite Prime's utter lack of actual fighting skill against a superior fighter, he was scary strong. Had Vegeta not have already powered up to his maximum when that blow had hit him, he would have instantly died.
Slowed by the pain, though he was, Vegeta still easily dodged Prime's next attack. The saiyan went back on the offensive, but as he fought, pounding Kryptonian from multiple angles each moment, he felt his strength slowly fading. Unlike Goku, who had conditioned himself to be able to maintain his Super Saiyan 3 state for an extended period, just maintaining the transformation was rapidly draining Vegeta. With that one blow from Prime, his time remaining in that form had been cut to a tenth of what he would normally be able to sustain.
And just like that Vegeta's power ran out. A furious Superman Prime lined him up for a life-ending punch. Just before impact, though, Vegeta disappeared.
Goku stood with Vegeta on the far side of the moon, one hand on the prince's shoulders and another with two fingers on his own forehead. "I guess that makes us even in this universe, eh Vegeta?" Goku said with a smirk.
De-powered, Vegeta glowered at Goku. "Why did you interfere? I would have defeated him."
Goku nodded, "Sure you would have, Vegeta. But, hey, since I did interfere and you didn't die, let's say we fuse and clean this guy's clock once and for all?" Goku pulled out a pair of potarra earrings. A birthday present from the Superme Kai.
Vegeta looked at Goku as if he had grown a new head. "Are you mad? Those things cause a permanent fusion! Do you want to end up fused with me forever?"
Goku grinned and waved one hand to forestall his rival. "I've left standing instructions with Krillin that if you and I ever fused like that again that he's to use a wish from the dragon balls to get us back to normal as soon as the threat has passed. We'll be back to our old selves in no time."
The Prince of Saiyans crossed his arms. "It doesn't matter. A saiyan fights alone."
"Look, you already fought him alone. So did I. We both proved that we could outfight Superman Prime. We've both beaten him. It's only because of his regeneration that he's still around. But if you go out there and beat him again you'll still have to admit that he's stronger than you. Stronger than any saiyan. Not more powerful, but stronger. Or, we can put on the earrings and show him what real power is."
Vegeta hesitated.
"I'M GOING TO KILL YOU MONKEY SCUM! Your whole race is PATHETIC!" called the voice of Superman Prime from the other side of the moon.
"Give me the damned thing," Vegeta swore, snatching the earring from Goku's hand.
From the dark side of the moon a white burst of light flashed out and the most powerful saiyan of all time was reborn. Vegito.
"Where are you, you piece of—"
"Right here," came a voice from directly behind the Kryptonian. The dual voice rang in Prime's ears and for a moment, the Kryptonian felt fear. But then he remembered that he had come out the victor in their confrontations. He was Superman. They were just monkeys. He spun around to throw a punch.
Vegito caught the punch in one hand.
Eyes widening in shock, he threw a second punch with his other hand, much harder than the first. But this time the punch wasn't caught. Instead, his fist made contact with his new opponent's chin just as Vegito's hair turned golden and Super-Vegito's eyes widened into a fierce green. Superman Prime's fist stopped and Vegito's head didn't even move.
"Wow, that was strong," Vegito's voice mocked. "That would have killed Prince Vegeta or Kakkarot for sure." Then Vegito struck back, snapping Prime's head around and drawing blood. "But then, I'm something else entirely."
Prime backed away from the fused being in shock. "Im-Impossible!" Then the Kryptonian clenched his fists, his rage building. Eyes glowing a deep red and screamed and charged back towards blue and orange clad warrior. Once again Vegito grabbed Prime's hands with his own. The pair struggled there, each trying to overpower each other using brute strength. To Prime's absolute horror, he found his strength almost perfectly matched.
"Incredible," Vegito mused. "Even with Kakkarot's and Prince Vegeta's powers multiplied together your strength is still equal to mine." Then a cocky grin spread across the fused-saiyan's face. "But the difference between you and me," Vegito said in his odd dual voice as their arms struggled back and forth, "is that I can do THIS!"
And with that, Vegito twisted backwards with his hands still locked with Primes, his feet shooting up through the gap between them to connect powerfully with the Kryptonian's head. Prime flew backwards through space, only to be intercepted by a confident Vegito. But instead of hitting Prime with a powerful attack, Vegito just slapped him across the face, spinning the shocked Kryptonian.
It didn't take Vegito long to tire of his game of toying with Prime. While they were now physically matched in raw strength, the disparity between there skill levels remained the same. While Vegito could block Prime's attacks with equal force, something neither Goku nor Vegeta could have done even at Super Saiyan 3, Prime still had no defense against the saiyan martial artist's strikes. And now every blow that hit him was crippling.
With a strike to the throat, Vegito left Prime sputtering in the void of space.
"I would leave you to learn your lesson, but I know if I do that you'll only come back and hurt even more people. For your insult to the saiyan race and for the sake of the universe, you have to die."
Prime whimpered, his hands coming up pleadingly as he tried to choke out some words. He would never get to speak them. There was no mercy for him in Vegito's eyes. The super being extended one arm down towards the Kryptonian, then the fused-saiyan's hand flicked up to form a right angle with the rest of his arm.
"FINAL FLASH!"
The resulting explosion would have wiped out the galaxy if not for its concentration into that one small section of space. The universe ripped open from the power of the attack but the blinding white power burned through the tears in space-time. There was no escaping to any alternate time or phase.
Prime was gone.
With a quick instant transmission back to the Earth's moon, Vegito found the Superman of this world. "Hi, there, Kal-El. Problem solved. Now, let's go find that Lex Luthor character. He owes my Kakkarot half a big dinner. And now I'm eating for two!"
Author's Note: This is an "alternate ending", a "what if", not a continuation of the story. I will be adding a few more of these, though most will be shorter than this one. I will also add another "Aftermath". But there is not time frame for the next one. It might be in a month. It might be in 3 months.