He made his first appearance of the season in the UEFA Europa League, coming on as a half-time substitute for Glen Johnson in a 1-0 win away to FC Gomel on 2 August.
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Flanagan continued his spell in the first team to cover for the long term injuries of Martin Kelly and Glen Johnson, making his second start the following weekend and playing the full match in a 1–1 draw at the Emirates Stadium against Arsenal, a game in which he accidentally knocked out stand-in captain Jamie Carragher through a clash of heads.
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Flanagan returned to the side on 24 March against Wigan Athletic in the Premier League in the absence of injured duo Glen Johnson and Martin Kelly.