I’m going to do a quick rewrite of the game’s story and make it something that I feel would have been more powerful and emotional. I’m not gonna be able to get into the details and continuity errors that result from my version. Yes it’s long, but I like getting this stuff out of my head and onto paper (in a manner of speaking). If you like it, please tell me! If you don’t, then that’s fine too. Here it goes. First off, the story will stay more or less the exact same right up to the part where MC and Locke have their showdown. Blue Team proceeds to teleport away to Genesis while Osiris is forced to evacuate Meridian.
Master Chief pushes Blue Team to their limits and beyond in his reckless hunt for the truth. Growing increasingly impatient, his temper catches the attention of Frederic and he begins to question John’s mental health. The hunt continues and Osiris eventually learns from the Warden Eternal that the Reclamation will begin once the Master Chief completes his mission. Upon hearing this, Locke realizes that John is being manipulated and is about to release something that could threaten all life in the galaxy. Osiris catches up to Blue Team on Sanghelios after receiving aid from the Arbiter and Locke attempts to reason with Master Chief from a distance. “Chief! Stop! I just want to talk. It’s Cortana, she isn’t real. You’re being manipulated by someone. You’re about to release something horrible, stop doing this before it’s too late! We can still figure this out together.”
Master Chief pauses to try and process everything but is overwhelmed by his emotions and unable to deal with them properly. He lashes out at Locke with guns blazing. “Blue Team! Shoot to kill!” A short but intense battle unfolds. Tanaka and Buck are seriously injured and the firefight ends with Blue Team collapsing the platform that Osiris is on. Fireteam Osiris plunges into the depths of a dark crevice and John wastes no time with moving on. “Form up, we’re getting out of here…”
En route to Cortana’s location via Pelican, an argument breaks out between John and Fred. “Those were people! Other Spartans! What has gotten into you, Chief?” Chief stares calmly ahead, not even phased by what he’d just done. “They were a threat to our mission. We eliminate threats…It doesn’t mater who stands in our way, they are a target.” Fred is taken aback. He steps backward in disbelief and shakes his head. “A threat to YOUR mission, not ours. I’m going back for them.” Master Chief tilts his head slightly and clenches his fist. “Are you compromising my mission?” He takes a step towards Fred but Kelly grabs his shoulder to stop him. Fred stands firmly in defiance. “Chief, I’m taking command of this Fireteam, effective immediately. I am ordering you to stand down and turn yourself in. You’ve gone too far.”
Chief throws a punch at Fred and a claustrophobic brawl unfolds. Kelly and Linda try to break up the fight but it gets too out of hand. Blue Team loses control of the Pelican and crash lands into a vast desert. Hours pass. Blue Team awakens to find that John is already gone from the crash site. Fred scans the area with the help of Linda and sighs. He turns on his wireless communicator and sends out this message: “This is Spartan Frederic-104 of Blue Team. Spartan Locke…do you read me?” The radio is silent for a long time but eventually a transmission comes in. “This is Spartan Locke, what is your location?” Fred responds with the team’s coordinates and Locke says one last thing before the cutscene ends: “The mission has changed. The Master Chief is to be eliminated by any means necessary…”
Chief is on his final stretch to Cortana’s location. At last, the truth will be revealed and the fight will be over. All that stands between him and revelation is a savage colony of Brute encampments. He can’t waste any time or risk being caught out in the open so he dons a cloak to help remain hidden amidst the rocky terrain. His training and experience serves him well here. He dips in and out of combat, making sure that no beast can set off an alarm. John feels, more than ever, that this is his destiny. Everything has lead to this moment as he approaches the hidden Forerunner construct. The blue lighting provides a comforting presence and Cortana’s whispers grow louder and clearer as he approaches a terminal in the center of a grand, open chamber. He places his hand on the terminal and Cortana appears with a blinding flash.
“John…” She says softly. “You’re finally here.” John stands in awe. “Cortana…What’s going on? Are you okay?” She smiles at him and replies: “We’ve been waiting so long for this moment…for the Reclaimer to arrive and begin the Reclamation.” Her voice changes, deepens and begins to sound sinister. “It couldn’t have been anyone else. We knew that you, of all people, could make it here while remaining faithful through the course of your journey…” Red lights begin to invade the room. All that was once welcoming starts to turn vile and repulsive. Danger. John knows he is in danger but doesn’t know what to do. For the first time in his life, he feels helpless and vulnerable. The ground begins to rumble as Guardians rise from their slumber. All of a sudden, John can’t move. His armor is locked up and the last thing you hear before the credits is Locke’s voice. "Chief. Oh God…what have you done?"
Game ends and the Legendary ending teases John being brought in by Locke. The story continues in Halo 6: Redemption.