How did Cobra Commander escape death after being shot in the back? Another Crimson Guardsman tailed the traitorous one and Raptor. When they left he undug Cobra Commander and took him to a doctor who also was a Crimson Guardsman (ah the Fred series).
Anyway, after surviving that thanks to the doc CC played it silent putting his Crimson Guards in certain positions ploting his return. Though during this time he also spent it selling Terror Dromes to foreign powers making a ton of money for Cobra.
And you say Hama wouldn't shoot Billy? The dude upon return, buries him and all his enemies and traitors in a volcano. After that when Billy continues to be a thorn in his side as others he brainwashes him with the that mindwave scanner Dr. Venom (along with the Baroness, he already tagged with hidden commands to return Destro and Zartan to loyality with it).
Not to mention does shoot Billy again in the first Devil's Due run. As some of the people said before CC lost the last parts of his sanity and humanity when that Fred shot him. It only confirmed to him you have to be truly evil to survive in this world. Hence his rutheless nature upon his return and since.