So you've all seen the Combat Evolved legendary ending, and you watched him die with the elite. Yet, despite this - he comes right back. There's only one logical explanation, there's a secret factory of clones. You know how you can kill him, but he just comes back after another pelican drop? Not to mention that he is immune to flood infection, a clone wouldn't register as a full senient body to host, so the flood can't use him. He is a spartan I after, the UNSC would obviously need a base spartan for reference to future programs, just in case. It's not hard to imagine they made these clones for that, and can spend them at will. Johnson always says suspicious things. "I'm to pretty to die!" He yells. Clearly this is true and clones are a way to preserve his divine beauty. "Back when I was in the core, we had a stick and a rock, and we had to share the rock!" You can tell here that the spartan I program was as ancient as cavemen, ONI is pretty secretive, it is highly believable that they had found forerunner tech back then, and used it to preserve Johnson. He refused to tell Guns how he got back in one piece. Surely the factory of clones is top secret, and no one can know. Johnson asks "why do you always jump? One of these days you're gunna land on something as stubborn as you are, an I don't do bits and peices." He is trying to warn Chief that falls like those can crush things, and as heavy as Chief is, Johnson doesn't want him landing on the factory, it would "bits and Pieces" Johnson. Halsey says in Reach, that Cortana is the key to winning the war. Evidently she runs the factory remotely, and without her, Johnson is lost. Not to mention he tells Chief to never let her go. This is because she can get Johnson back after they escape Halo, but after everything, Cortana dies without a way to get another clone to Requiem. Now that she's dead, the factory is at a standstill, and Chief needs to somehow bring her back to life, so she can use the clones again, an win the war against the forerunners. Johnson is after all, the key to it all.