Re: "even though I am not aware of any wrong doing on my part"
Careful - that's close to libellous. It's not established that he knew anything about how his engine design people were progressively "improving" the performance of the engines. There's no reason he should have known, he could have been as much deceived as the government's regulators. I'd fault the regulators to a greater extent, because their remit should have included catching out any cheats.
Somebody fairly high up the company must have known, and not passed any concerns up the chain of command. The chief resigned, because the buck stops at the top. He's resigned, because he clearly didn't sufficiently instill the importance of ethical behaviour in his underlings. He's resigned, because the board has lost confidence in him. The next CEO must find out who knew what, and fire those whose decision-making embraced wholesale deception as legitimate.