OK So heres my possible theory for the Halo 5:Guardians Plot.
Master Chief has gone rouge (obviously as he is hiding, in my opinion I believe he is hiding from the UNSC) to find Halsey so she can make a new Cortana. ONI has dispatched the new spartan to hunt down for John so he could be captured and be killed if necessary. Halsey on the other hand is preparing to strike at the UNSC for the planned assassination and revenge blah blah blah. So, John finds Halsey but Halsey is forced to run from John due to the Spartan and a bunch of UNSC troops after Master Chief. They all escape, the end.