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A debatable refereeing decision proved costly as Gillingham had a man sent off and their early goal advantage wiped out.
Vadaine Oliver put Gillingham ahead but Stuart O’Keefe was sent off for a second bookable offence - the second for an adjudged foul on Scott Twine, who converted from a penalty rebound. Peter Kioso then put MK ahead before Troy Parrott and Max Watters sealed it late on.
Gillingham had a trio of players struggling to be fit for the weekend and neither of them made it. The Gills also ended up without lively winger Mustapha Carayol - the star of the previous week - and had to make a change with O’Keefe replacing him in the eleven.
The Gills were once again short of numbers on the bench, with teenage striker Gerald Sithole returning to the squad.
Despite the unexpected selection issues the Gills were well in the game early on, Kyle Dempsey going close with a shot seconds in. The visiting keeper had to save with his legs.
Troy Parrott was denied by Gills keeper Jamie Cumming but the Gills were to take a 20th minutes lead, Dempsey doing the hard graft in midfield and sending Alex MacDonald away down the left. MacDonald had a shot blocked but when the ball fell back into his path he dinked over a cross that Oliver nodded home.
It wasn’t long before things took a downward spiral for the Gills.
O’Keefe was booked for throwing the ball away and moments later was then penalised for a foul on Twine inside the box. Referee John Busby sent the midfielder off.
Twine was denied from the spot by Cumming but he was able to stick away the rebound with Gillingham players closing in.
MK Dons then managed to take the lead, 11 minutes later. It was a neat finish from Kioso into the top corner, turning away from David Tutonda as he latched onto a ball from Matt O’Riley before finding the net.
Gillingham had reshuffled following O’Keefe’s dismissal with Oliver left alone upfront and Ben Reeves replacing Charlie Kelman. Boss Steve Evans made a tactical switch at the break, taking off Tuntonda and playing the second half with three at the back.
Evans tinkered again 10 minutes after the restart having watched MK start the second half in dominant fashion. Striker Gerald Sithole replaced midfielder Dan Adshead.
Sithole had claims for a penalty turned down on the hour mark after keeper Andrew Fisher came racing out to challenge him. The Gills youngster went down in the box but the referee wasn’t interested.
Gills captain Dempsey drove the Gills on and with Sithole’s pace they began to make it uneasy for MK. A weak passback from O’Riley almost led to another Oliver goal but goalkeeper Fisher managed to make a brave save from the Gills striker.
The Gills kept pushing and Oliver watched as his superb volley was tipped over by Fisher. From the resultant corner Ehmer had a shot blocked.
Former Maidstone man Max Watters could have sealed it for MK at the other end, in on goal with just the keeper to beat, but the substitute was unable to get past the legs of Cumming.
Parrott ended Gillingham’s hopes of a fightback with a third MK goal on 82 minutes, scoring from an angle and aided by a deflection off Max Ehmer which took it past the home keeper.
Watters made it 4-1 in the 88th minute after Twine slipped the ball into his path, his first effort was saved but the second was fired into the net.
Gillingham: Cumming, McKenzie, Tutonda (Bennett 46mins), Ehmer, Tucker, Adshead (Sithole 55mins), O’Keefe, Dempsey, MacDonald, Kelman (Reeves 37mins), Oliver. Subs not used: Chapman, Lee, Lloyd.
MK Dons: Fisher, Lewington, O’Hora, Darling, O’Riley, Twine, Robson (McEachran 85mins), Boateng (Watters 60mins), Parrott, Harvie, Kioso (Watson 76mins). Subs not used: Ravizzoli, Jules, Brown, Martin.
Referee: John Busby
Attendance: 4,119