its probally a bit late but here is the most logically theory possible at one of the last terminals in anivarrsary 343 guilty spark said he might be able to manipulat the covenant and the unsc minds in order to light the rings but also several times guilty spark had teleported cheif around the rings. so maybe 343 guilty spark teleported johnson to safty and the elite to safty. b ut why the elite because maybe the elite is arbiter and maybe arbiter was there at the last stand of noble six .arbiter is left handed. in halo 2 a litttle after arbiter became arbiter. johnson and arbiter keep calling themselves as arch rivals as if they met each other before. and another answer to the question how did johnson survive the flood? will power. the flood is a parasite with a mind enough will power will kill it. in anivarrsary keyes had almost been free of the flood but had not much will power left so he was succumb over a huge pure flood form. now that explains that.