The St Mary’s Stadium club have secured Downes from London outfit West Ham United.
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The 25-year-old was on loan at the club last season, excelling in their Championship run to the playoffs.
"We’re thrilled to bring Flynn back," said manager Russell Martin.
"It was a big priority for us this summer and to get it done early in pre-season is also really important for us.
“He was such an influential player for us last season, both on and off the pitch.
“He’s a brilliant character, he’s aggressive and physical in his play, technically excellent with the ball and a fantastic athlete too."