An alternate Halo 5 plot:
Okay, so the game begins in a similar vein to what’s discussed in the comics. Chief is struggling to come to terms with Cortana’s loss and driving himself to self destruction on various missions. When on one of those missions, we get to see him fight the Covenant and how forlorn he and reckless he is over this. Its during this mission that Cortana attempts to contact him.
Rather than a full dream where she reveals herself, the player and Chief is left second guessing. Much like at the start of Reunion, Cortana uses lights and sounds to communicate with Chief and tells him to go immediately to this place. Which we later find out is a Forerunner Broadcast beacon. Cortana needs Chief to activate several of these across the galaxy to free her from the Domain and use the Guardians.
Chief doesn’t do this right away and goes back to Laskey aboard Infinity. He explains that he thinks Cortana contacted him and they discuss what little they know of the Domain. Chief is adamant that she must be alive and wants to be involved. Laskey cautions that theres no proof its her, shes almost certainly dead and the Chief isn’t thinking clearly. He orders him out of action.
The Chief decides that he is personally responsible to Cortana, especially remembering what happened at the end of Halo 4, is unable to accept her death and takes matters into his own hands. This is when he goes AWOL and he escapes the Infinity in a stolen vehicle. Laskey orders Locke and Osiris to go after him.
The first world is Meridian. The world is under attack by Jul M Dama and his Promethean army. Chief saves as many people as he can before reaching the underground vault. He activates the beacon just as Jul’s army approaches and after his first confrontation with Locke. As he does this, the Prometheans on Meridian turn blue and violently kill the Covenant forces. However, during this a Guardian awakens and fires its EMP pulse destroying a human city in the process. Chief is horrified by this but convinces himself that Cortana would never have deliberately done that and must have limited control over the Prometheans. He is given the next set of co-ordinates on Sanghelios and travels there, convinced hes doing the right thing but troubled.
It switches back to Locke who is enraged that he couldn’t stop Chief and personally blames him for whats happening. Convinced that it is indeed Cortana and that Chief is being a fool he decides that the Chief must die; irrespective of what Laskey says. As far as Locke is concerned Chief cannot be convinced that Cortana is evil.
Sanghelios more or less plays out similar to the events in the game except the Chief has to convince the Arbiter to help him. The Arbiter kills Jul M Dama in personal combat and achieves victory over the Storm Covenant. Before this we see Jul and Halsey increasingly panicked as more and more Prometheans activate and turn against them. Jul’s effort’s on Sanghelios are a last desperate gamble and this foreshadows the looming threat of the Reclamation. Halsey is recaptured by Osiris as Chief escapes on the Guardian to the final co-ordinates as it beckons him. She reveals everything she knows about Cortana to them and begs Locke not to kill the Chief; reminding him what the Chief did and that he would never betray humanity. Locke is troubled by this but still appears committed.
Chief arrives on Genesis and it plays out similar to Reunion except that he doesn’t speak to Cortana. Instead he finds the Warden who torments the Chief. At this stage Cortana has what she wants and so he is not troubled with killing him. He enjoys tormenting the Chief and sadistically tries to convince him that he was behind the whole thing; that Cortana really is dead and he betrayed his race for nothing. Chief is enraged, says hes not a traitor and knows hes lying about Cortana and so presses on; still guided by Cortana. He refuses to believe that Cortana could do any of this and that the Warden has to be behind this. Locke, in another mission, is able to reach Genesis, and attacks the Chief. They have an extremely violent clash in which Chief wins and leaves Locke; deciding not to execute him. Plays out similar to the trailer but he walks away through the portal to the Domain; convinced that he can save Cortana from the Warden. Finally he meets Cortana in the Domain and realises that she is in full control of the Prometheans and the horrifying extent of her plans. Cortana tries to tell John that shes not a monster, means to do the right thing and is sorry for misleading him to do this; yada yada. The Chief refuses to help her and attempts to convince her to stop.
Switch back to Locke, who recovers and has all the anger drained out of him as he realises that Cortana must have lied to Chief and would only lock him up if he was a threat. Putting humanity over any thought of revenge or shame he rescues the Chief. Game ends much the same as Halo 5.