Unfortunately couldnt add more chapters to the rest of the story so It'll be continuing here separately.
Here is the continuation I promised. Updates likely won't be very fast, but they'll each have maximum effort.
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Deep in space, far into the infinite cold expanse, an earth-like planet thrives. Created under very similar circumstances to Earth itself, it bred similar life. Although the introduction of foreign life-forms forever diverged its course. And soon enough, over a millennium later, more foreign beings were going to visit it. One of these beings examined the planet from the confines of his ship and stated, "This sector of the universe is... unique. Its gravitational yield exceeds what's typical for most sectors bearing life. And the cause of the black hole orbiting this solar system belongs to this very planet."
Small alerts echoed through the empty yet vast ship and the man veered his head to cameras showing two pale men flying through space, "More visitors? Interesting."
On Itachi's new home planet, Earth. The five-year war has finally ended, and Superman was stripped down to Clark Kent, just a man in a cell with red sun radiation. Its rays seem to bathe every surface in a sheen of blood, courtesy of Batman. The only stimulation the man was offered for the time being was books and the constant mechanical hum of machinery that was inescapable. While sitting on the bed, he hunched over, hands held together. His conditions felt cold like the bed, yet deserved.
Beyond the confines of the circular glass cell, a door opened, and his eyes widened as he gazed upon a long-lost sight. He shot up to his feet, and his voice matched his wide eyes, "L-Lois?!"
The door opened automatically for Lois who strolled in with a mixed smile for the love of her life, "It's me, Clark."
Superman's hands twitched and Lois observed it before spreading her arms wide, "Come on."
He embraced her without hesitation and a tear dropped down his cheek, while they both smiled. She commented, "Just so you know, you look much better with the curly bang over this hairstyle."
He snorted and they lightly separated while still holding each other's arms. Superman was filled with joy, but the cold touch of Lois's skin made something in him stir. "I'll have to bring it back... But Lois, how are you here?"
She loosened her hold of Superman's arms and her smile weakened, "Itachi has... temporarily brought me back through some kind of technique. I'm alive, but... not really."
His smile disappeared and she continued while looking away, "He... told me what happened in the past five years since I died too... The Joker..."
His jaw tightened, "The Joker had to go..."
She cupped his cheek, "I'm not saying he didn't, but Clark... everything that came after that..."
He lightly held her hand and his face softened as the silence stretched on, "... Yeah... I tried to control everything... I just thought that... maybe if I could stop all the senseless violence then... then no one would have to go through what we did..."
Lois replied, "But things weren't that simple, were they?"
He looked down, "No... a lot of people suffered... I had a couple of enablers pushing me on but... ultimately I was always the trigger in the end..." His face went downcast, "I hurt and killed a lot of people, Lois. Innocent people."
Lois pursed her lips, but after a moment she lifted his head upwards to meet her eyes, "The Clark Kent I married would never make those choices, but he also never had to watch his wife, unborn child, and city all die."
"Does that excuse what I became?"
"No... but it explains it... the question now is just what you'll do moving forward now that you see clearly again."
He slowly sat down with his hands on his knees, "I... don't know. I don't know if it's really possible to come back from what I've done."
She sat next to him and smiled, "Of course you can come back Clark, I can still see the man I love clearly in those eyes... You have to start with the people you can help. Not through fear and control, but with hope. The way we used to believe it could be done."
He held his hands together and stared at them, "I don't know if the world could ever forgive me..."
"Forget about the world for a moment, do you even forgive yourself?"
His gaze met hers, "I... don't know if I can."
She took on an expression that always used to melt his heart, "Then there's your start. One person at a time, one day at a time. Starting with yourself."
Clark's smile met her own, and at least for the moment, the red sheen bathing the room lost its malicious association in his mind. "You're right, I'll try."
She replied, "Great... and well there was one other thing that Itachi told me about."
"What's that?"
She tilted her head with a raised brow, "Can you tell me about how that bitch Wonder Woman was trying to steal your heart along with your morals?"
Over the course of multiple days, Lois and Clark talked, laughed, and cried together until Clark finally felt at peace. After the jutsu was undone, Superman spoke with Itachi and developed a new conviction to live his life by for the foreseeable future.
Although before he could start thinking about going back into the world, he had one last conversation to go through. Across from Clark sat the first member of his species he'd met that wouldn't try to kill him. His eyes remained wide, and the recognition blocked out the white noise of machinery that had kept him company.
She sat across from him on the stool on which he had previously held his books, and she anxiously held the sides of it. "Kara..."
Her wandering eyes turned to meet his, "You recognize me?"
He nodded, "I've seen your image on my ship before. You're my cousin. You were supposed to be my protector."
She brushed some of her hair aside, "Yeah... sorry for being a few decades late for that part. A lot has changed since then..."
Clark's chest tightened and he looked down briefly, "That it has... sorry we had to meet for the first time this way... How long have you been on earth?"
"A week... I've been told a lot of things since I've been here... How you went from the greatest hero to a monster... What happened to Metropolis... All of it."
"And what do you think of all that?"
"I think... It's scary. That it isn't the Kal-El I expected to meet at all... I've been told that that should be in the past now though. I'm hoping that's true." She stared at him intensely.
He nodded, "I plan to put it behind me."
A cautious smile spread on her face, "I... really want to believe you. But it's everyone else that really needs the convincing."
"I plan to do whatever it is I can to regain the trust of people."
While their conversation went on, footsteps approached from outside the cell and the kryptonians turned their heads to see Itachi approaching. He opened the cell and walked in with a wave.
Clark stood up and offered a hand that he shook. "You look much better than last time I saw you."
"Talking to you, Lois, and now Kara has helped a lot. I really can't thank you enough."
"That was the goal. If you wanna thank me, you can do it by being a man to look up to again."
"I agree, but I doubt I can just walk out of here and put a cape on again though."
"Definitely not. The path will be hard, but—"
"—There will be no path to take, Itachi." Amanda's voice cut through the air and the three turned to see her striding into the room with two armed men on her flanks.
She sized them up, "Last week's world Dictator, our currently allied government obstructing wildcard, and the object that crashed landed from space a week ago."
The three gave her scowls of varying degrees but kept their cool. Itachi greeted her, "Director Waller. A pleasure."
She raised her hand, "Don't give me that fake respectful tone. We know what you heroes have been planning. Some kind of grand rehabilitation scheme? Sorry, but you people need a reality check. The world isn't a Congregation welcoming sinners with open arms."
She stepped forward with a demanding presence unbecoming of her stature and pulled out a tablet from inside her suit, "84 countries so far have formally requested that Superman remains imprisoned for the rest of his life, the UN Security Council has three separate resolutions calling for his permanent imprisonment, there are active petitions with over a billion signatures so far calling for a life of imprisonment, and multiple world powers like Russia and China have stated that releasing Superman would be considered a direct act of war on their sovereignty as nations."
Supergirl tried to speak up, "Amanda—"
"—I'm not done yet." Supergirl's growing scowls was ignored. "Superman's regime had a massive effect on the entire world. Every family in the world is only just now getting a taste of not being under its boot after years. Do you people comprehend the kind of global catastrophe that would happen if Superman were let free? So no, there will be no rehabilitation. No second chances. No redemption arc. Superman spends the rest of his life in this cell, dies, and then the world moves on. We don't need him anymore. Especially if another one of his species came to replace him."
Silence fell in the room, and Superman looked down with pursed lips. The glimmer in his eye dulled out at the revelation that was blasted in his face. Itachi was the only one to remain nonreactive.
Supergirl reeled back with the side of her lips raised and was ready to speak up, but a shadow dropped from the ceiling and landed without the slightest sound. The guards turned their weapons towards the unexpected visitor, but the man raised his arm, cape settling around him, "Stand down."
Amanda glared at him, "Batman. Of course, you would be lurking around here. Come to advocate for your old friend?"
"I've come to discuss a solution that will serve the interests of everyone on Earth."
She crossed her arms, "And just what could that be?"
Batman straightened up and came closer, "You're right that releasing Superman now would destabilize the world, but you're wrong about one thing. The world still needs Superman. Not the Superman that ruled for the past five years, but the one that used to be a symbol for the world."
Amanda scoffed, "Like that will ever happen again."
"Even if he never gains his old reputation back, he's needed regardless. Earth has experienced almost ten different hostile alien invasions in the last decade. And we would have lost most of them without Superman. Considering how Darkseid's son was killed, he could come back, trying to seek vengeance, at any time if he wanted. And there's likely more hostile threats out there we're yet to see."
Waller replied, "I understand that, but there's clearly another Kryptonian around now that can fill that role."
She pointed toward Kara and Itachi added, "Kara isn't nearly as strong as Superman is. Superman is only as strong as he is because he spent his entire childhood soaking up yellow sun radiation. Considering that Kara has only been on Earth for a week, it would likely take her years to get to that level. In that time we could have another world-ending event that'll destroy us all because Superman couldn't help."
Waller remained silent, then raised a brow, "We couldn't just release Superman at these specific times when he's needed then?"
Batman answered. "It's possible, of course, yes. But it's better to cooperate with a Superman willing to change than dealing with a disgruntled Superman that we only use as an attack dog..." Batman's gaze briefly turned to Superman, "If... we all turn our backs on him when he's reaching out, it could end poorly."
Superman looked up at Batman and Waller gripped her arms and closed her eyes for a moment.
Itachi added, "I can also say that Superman's chances of becoming evil again are close to zero. I'll try to tell the UN Council formally, but the ability I used on him wasn't some form of hypnosis or an illusion. It's a trap. It's not possible to escape from it until said person accepts the reality of their mistakes. It's so powerful that it comes at the cost of my eyesight in one eye."
Waller stayed silent for but a moment before sighing heavily, "Fine... I see what you're going for. Let me guess, you already made up some kind of plan on how you'd reintegrate him?"
Batman answered, "We made a four-stage plan. He'll start out with having power dampeners on 24/7 with military and satellite oversight at all times. He'll do mundane community services as a normal man, nothing glamorous. After he's spent enough time doing that, he can move up to things like disaster relief and some basic hero work that allows him a little access to his power, still supervised, of course."
Itachi continued, "For the third stage, he'll have limited freedom. A parole of sorts. He'll have limited times of the day when he can move around freely and have access to a lot more of his power. At this stage, he'll be able to help out with anything. If he ever steps out of line though, then he'll be finished. No third chances."
Amanda asked, "And the fourth stage?"
Batman answered, "Full freedoms. Back to what he used to have years ago. This might take years, but if we don't start this process now, we. We'll wish we did not if, but when another threat comes to try and dominate us."
Amanda's expression gave away nothing, eventually speaking, "You two are responsible for this. If he ever reverts to his old ways and it blows up in our faces, it'll be on you people!" She pointed at both Itachi and Superman as she and the guards marched out of the room.
"Understood." They spoke in unison.
Once the heroes were left alone, there was silence accompanied by the room's white noise until Batman cleared his throat. He removed his cowl and turned to face him with a soft look.
Clark, caught off guard by hearing his human name, waited, and Bruce drew a breath while stepping closer, "I need to say some things... things I should have said years ago... I never said I was sorry... about Lois. I failed you... When you lost Lois and were growing in grief I should have been there." His lips tensed and he briefly looked down. Clark's own expression softened while he paid full attention, "I was foolish to expect you to just... handle it. I got too focused on maintaining moral boundaries in the moment... and I held you to an impossible standard as if you weren't as human as the rest of us, and ultimately... I contributed to what you turned into."
Clark spoke softly, "Bruce..."
"Let me finish. I'm sorry that it took losing you completely to realize what I did wrong, I'm sorry for not being there when you needed me most, and I'm sorry that it took until Itachi helped bring you back for me to finally say any of this. I held up my pride as more important than being even a little sympathetic to you... and that has been one of my greatest mistakes."
A genuine smile crossed Itachi's face, and Kara looked between the two curiously but smiled as well. Clark took a step toward Bruce and pulled him into a hug, "Bruce... thank you..." His voice was raw. "I made my own choices, you're not responsible for what I became."
They separated and Bruce replied, "No, but I played a part in it. And moving forward maybe not as friends, but at least as allies, I wanted you to know I saw my own mistakes too."
Clark smiled, "I forgive you, Bruce. And I hope you and everyone else will be able to forgive me one day too."
Bruce put his cowl back on with a slight smirk, "Earn it, Clark."
"I will, no matter how long it takes or how hard it is."
Batman turned to leave, and Itachi stated, "In that case, let's start the program in a week. I have a feeling the nations of the world will be on board with the idea."
Kara asked, "So how are you gonna present it to them anyway?"
Itachi explained his plan to Kara, and while he did that, Clark felt genuine hope. It's not guaranteed, but he's really close to getting a second chance. And he'll do anything he can to prove he's not who he used to be.
Within a couple weeks, Superman's rehabilitation process began. While the world began watching Superman again, itachi turned to a more personal matter.
Under the cold crystal architecture of the Fortress of Solitude, Itachi and Zatanna conversed.
Zatanna hung her arms around his neck while he typed on the computer next to the Phantom Zone Entrance. Despite all the war, losses, and uncertainty of the future, this at least felt right, "Are you sure about this?"
He entered one last key that made the portal come to life, emitting particles at the edges. "I am... I think the Sage who originally sent me here somehow knew what would happen and sent me to help. Now that I've fulfilled that purpose, I think I can go back where I came from..."
Zatanna frowned, "You make it sound like you won't come back."
Itachi turned to face her and tapped her forehead in a practiced gesture, "Sorry if I worded it that way. Of course I'm coming back. This is still my new home, but I want to see how everyone's doing back where I came from."
Zatanna's smile returned, and she held the hand that had tapped her forehead. "What was that?"
He smiled widely, "Old habits die hard," He turned to the portal and approached it, "I could bring you with me next time."
"I'd like that, but for now I'll keep watch on the entrance. Better safe than sorry, even though there aren't any reports of life left in there."
They waved at each other as his body went through the portal, and once on the other side he was once again greeted by the familiar stale feeling of his body being in stasis. Although it wasn't imprisonment this time. He gathered in his surroundings, feeling a weird sense of nostalgia from the floating rocks scattered across the purple abyss of infinite space.
His eye caught a glimpse of a pristine building structure in the far-off distance, 'That'll make this easier.'
He heard Zatanna's voice echo in his mind, "Do you hear me?"
"Loud and clear." Itachi sprouted Susanoo wings and began his leisurely trek back to that familiar place.
"So how's it feel being in the Phantom Zone?"
"About the same despite my lack of injuries this time."
His Sharingan activated and he analyzed the multitude of rifts as he passed them. Zatanna asked, "That would match up with what I've heard about the dimension. How do you know which rift will be the correct one anyway?"
His eyes tore apart the hidden layers of the rifts, revealing their truths, "Last time I was here, I noticed there were two distinct types of rifts. Most were these chaotic wavy tears in space. Fluid spaces that I was able to see what I wanted through."
"Is that how you saw what was going on with Constantine a couple years ago?"
"It is. Besides the tears though, there was one that was like a blank glass pane. A camera constantly observing something."
"And that one was the one you saw your world through?"
"Yes."
"Exactly."
His feet made no sounds as he landed in front of the old base. He entered the sterile empty building and recalled memories from his last time here to go straight to his goal. "I'm inside now. Should be in the main lab."
"Good luck."
He took a different route to the room than last time and strolled past two large glass shards, one showing a world where Superman wore a sickle and hammer on his chest instead of an S, and another showing a world where Batman's mom was alive... and he was 6'9 for some reason.
Then, finally, he arrived at the room where he and the Titans once charged the ecto armor in. He couldn't suppress a smirk as he observed the familiar orange broken glass, "I've found it..."
Zatanna smiled, "That's great!" Itachi approached the rift and Zatanna continued, "I'm not sure if I'll be able to maintain a connection when you crossover, so make sure to tell me how things—"
"It's gone."
Zatanna's breath caught in her throat, "... What?"
A deep chill ran down Itachi's spine, and his smile disappeared as his Sharingan burned through the image of not konoha, not the world, but only dead space, empty coordinates. "... It's gone... there's nothing here..." His voice was hollow.
Zatann's brow furrowed and she replied softly, "Maybe your hypothesis was wrong?... or it's in a different—"
Itachi cut her off with a depressed scoff, "Zatanna... I've seen these stars thousands of times... I've memorized all of the patterns... this is the same nightview I grew up seeing…" He kept looking around as if what he saw would change, but that was in vain. "There's no chakra. No moon. No planet..... It's gone."