Thanks to all the Halo and Naval tutors who helped me with the protocol on this page, I've taken your advice and done the research and now we've got a more accurate and believable version of MC's arrest. Emergency Priority Order 098831A-1 is the Cole Protocol and Article II subsection 7 states that no Covenant ship (or other tech) can enter UNSC controlled space without making sure that all traces of Earth's location are either destroyed or removed. Meaning that keeping that ship in the woods and the AI unit in the camp could have provided resources the Covenant could use to find Earth. It would be adequate reason to remove a CO.
I wasn't originally going to have the Chief hit him, honestly, but you guys were so adamant about beating the crap out of him that I included a good pistol whip in before we incarcerate him. Honestly, it's easier on me because now he's unconscious and I don't have to worry about writing him lines.
And yeah I know, a pistol whip from Master Chief has killed in the past but for my sake just accept that he pistol whipped him lightly so the Captain has probably got a hefty concussion but no permanent damage short of a little memory loss. Chief's not in his armor, so doesn't have that added force in there either. Don't yell at me please...