Coulson's situation was far from good, but he still held on. One reason he had been able to endure the harsh living conditions and the US Army's rabid pursuit was that he did not want S.H.I.E.L.D. to disappear just like that.
Although S.H.I.E.L.D. had been set up by Hydra this time, although it had nearly brought a terrible disaster upon the world, and although it had to answer for many terrorist operations over the past few decades, he knew S.H.I.E.L.D. was still a good organization.
He knew that some agents were still innocent, that their ideals and aspirations had never been this. He did not want S.H.I.E.L.D. to be destroyed under such infamy. He had to do something.
The second reason was to continue fighting Hydra. In truth, those two reasons could be combined into one: to clear S.H.I.E.L.D.'s name, he had to fight Hydra. That was also why he had left Talbot behind and run off on his own. It was not that he did not know what consequences such actions would bring, but he understood even better that words were weak and powerless.
When something like this happened, no amount of explanation would help, especially with the US government, which had always practiced hegemony. Would it listen to your explanation? If it had not shot first and asked questions later, that was already because the intelligence in your head was still useful.
So surrendering and staying behind to go through official procedures would not only waste time, but accomplish nothing. It was better to use actions to demonstrate his position. As long as he produced tangible results in striking Hydra, that would be more effective than a thousand words.
And who would Coulson focus on in his fight against Hydra? It could only be John Garrett!
It could