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Wotton joined Plymouth as a nine-year-old and rose through the ranks to become captain in the 2001-02 season when they won the old Third Division championship.
He was still skipper when he guided them to the Second Division (now League One) title in the 2003-04 season.
"I'm very emotional that I won't be playing for the team that I love anymore," he said.
"It's a deeply emotional day but when one door closes another one opens and you have to look at it that way.
"What's done is done, but the overriding factor is that I'm immensely proud of everything I've achieved at Plymouth Argyle."
Wotton has been struggling with a knee injury for over a year but finally made his comeback for the Argyle first team against Burnley in February.
And he says he has no plans to hang up his boots: "One thing's for sure, I'm going to be playing football at the highest level I can play.
"I'm 30 years old and I've got a lot of football left in me, I'm also excited by a fresh challenge.
"I'll be working at another club, wearing a different kit and these are things that I've got to be excited about."