He had a clear conscience, for his hands were clean.
He went on vigorously with his work, though he knew that the inquisition against him was at its full height.

His enemies reported that he was "no artist, and that he was altogether insufficient to perform such a service" as that of building his great ship.
Nevertheless, he persevered, believing in the goodness of his cause.
Eventually, he was enabled to turn the tables upon his accusers, and to completely justify himself in all his transactions with the king, the Lord Admiral, and the public officers, who were privy to all his transactions.

Indeed, the result of the enquiry was not only to cause a great trouble and expense to all the persons accused, but, as Pett says in his Memoir, "the Government itself of that royal office was so shaken and disjoined as brought almost ruin upon the whole Navy, and a far greater charge to his Majesty in his yearly expense than ever was known before."[24] In the midst of his troubles and anxieties, Pett was unexpectedly cheered with the presence of his "Master" Prince Henry, who specially travelled out of his way from Essex to visit him at Woolwich, to see with his own eyes what progress he was making with the great ship.
After viewing the dry dock, which had been constructed by Pett, and was one of the first, if not the very first in England,--his Highness partook of a banquet which the shipbuilder had hastily prepared for him in his temporary lodgings.
One of the circumstances which troubled Pett so much at this time, was the strenuous opposition of the other shipbuilders to his plans of the great ship.

There never had been such a frightful innovation.

The model was all wrong.