He could smell the blood.
Even through the driving rain, over the dominant smells of rotting wood and seaweed, that sickly scent was still there. The rain washed away most of the blood that appeared from the lacerations to William's back, but still it welled sluggishly, but still Bootstrap could see and smell it, and realise where his life had taken him and his son.
He remembered a time when he wouldn't have even believed in things such as the ship he stood on, the crew he worked amongst or the thing he was slowly changing into. Or that damned curse that led him to the Flying Dutchman in the first place.
He saw the pain and disgust in William's eyes. Felt William's anger towards him. Practically taste it. When the curse laid on him by the Aztec gold had suddenly been lifted he'd assumed the worst concerning his son, knowing the last coin had been in his possession. Had hoped that his leaving would ensure a better life for William, and through it all he'd still somehow managed to fall in with Jack Sparrow of all people.
And now his son stood before him, a man. Bootstrap felt a pang of sadness for having missed his son growing up. As soon as he fell in with Barbossa and his crew, he knew it would end badly, could see what sort of a person Barbossa was and what he'd do to his wife and son if he ever found out they even existed. If he ever had reason to question Bootstrap's loyalty. Bootstrap had instead found out firsthand what would result from that.
Bootstrap saw the disgust and anger turn to pity. Saw the plan forming in William's mind when Wyvern revealed the secrets of the Dead Man's Chest. He felt pride when he looked upon his son's face and realised the man he had become. Though he was never told, he could see that William was in love, as plainly as daylight shining through clouds, and knew whoever she was was a lucky woman. Just as he had been lucky to have once had a wife such as his.
He fought to contain the sorrow. Davy Jones forcibly held him so he had no other choice than to watch the ship that William had escaped to be crushed, broken, and dragged down to the depths by Jones' monstrous Kraken. Bootstrap had never laid eyes on the beast, and he didn't care to now, not ever. Jones seemed to be in such a murderous mood he had his crew slaughter the 'survivors' without so much as asking his age-old question. Bootstrap, despite it all, was glad William hadn't survived; if he had, Jones' wrath would have been unquestionable, there being no telling what he would have done.
Bootstrap had felt a lot of things over the years. Despair had been predominant in his un-life until those short days ago when his son had reappeared in it, and shown him what it was like to be a father again. Reminded him of what it was like to love.
William Turner, otherwise known as Bootstrap Bill, watched the last of the wreckage sink beneath the waves. Tried not to think of how futile it had been to attempt to go against the will of Davy Jones. And offered a short prayer for the soul of a son that should have never had any part in this.