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Gillingham were humbled by non-league Brackley Town in their first round replay.
Jimmy Armson scored twice in ten minutes to stun the Gills but they got a lifeline before the break with Jake Hessenthaler’s goal.
Brackley wasted a number of good chances before substitute Scott Wagstaff pounced to level the scores in normal time.
Cody McDonald turned Shane Byrne’s corner into his own net in extra-time and Armson further embarrassed the Gills by completing his hat-trick.
McDonald pulled a goal back deep into extra time but Gillingham couldn't find another equaliser.
Reaction: No positives whatsoever, says boss Justin Edinburgh
The Gills had got some form back of late, ahead of the first round replay, with wins from their previous two games, but were deservedly beaten by National North side Brackley on Wednesday night.
Bradley Dack returned to the starting XI for the Gills, replacing injured Frank Nouble (hamstring). Paul Konchesky and Bailey Cargill were left out.
A trip to Blackpool was the carrot for the victors, with a chance of making it to the cherished third round and a possible money-spinning tie.
Just like the last time they met, Brackley took the early initiative, as Gillingham’s defence was exposed by the part-timers.
Lee Ndlovu and Glenn Walker both had half chances early on for the hosts before Armson opened the scoring on 17 minutes. The Gills were slow to react from a free-kick and he pounced.
The Gills found themselves two goals down in the 26 minute when Brackley hit the visitors on the break. Emmanuel-Thomas lost possession in attack and Armson played the ball out to Steve Diggin and then finished the subsequent cross.
Gills boss Justin Edinburgh abandoned his starting formation, putting Dack back in his more natural central position, at the top of a midfield diamond, and it didn’t take long for that switch to pay dividends.
Dack picked the ball up centrally and when his shot was parried by the keeper Laurie Walker, Hessenthaler was on hand to crash the ball home from an angle.
The Gills had got themselves back in the game but Brackley finished the half with a couple more chances, leaving Edinburgh’s men with much to do in the second half.
Captain Josh Wright was introduced at the break, replacing Chris Herd, who picked up an injury late in the opening half.
Gillingham started the second half positively but were unable to back it up by testing keeper Walker. There were appeals for a penalty when Dack went down in the box but referee Robert Jones waved play on.
It wasn’t long before Brackley began to threaten again. Oshilaja had to make one vital clearance and a floated effort from Armson was almost prodded at goal by Ndlovu.
Ndlovu had a couple of close efforts in as many minutes around the hour mark, as the Gills defence struggled to contain Brackley. They looked vulnerable every time the hosts went forward. Armson put a great chance over, as the hosts kept probing.
The Gills survived the flurry of attacks and then got on level terms with Wagstaff firing home at the near post, just seconds after replacing injured Garmston. It was all-square with 67 minutes gone.
Gillingham looked more assured after the equaliser, helped by Wagstaff’s energy, and pushed for a winner in normal time, which they couldn’t find, as the tie went to extra time.
Brackley went back in front on 96 minutes when Shane Byrne’s inswinging corner went in via a deflection off McDonald.
It got worse for the Gills at the end of the first period of extra-time as Armson swept the ball home to make it 4-2.
McDonald rounded the keeper to pull a goal back late on but Brackley did enough to see the game out.
Brackley: L Walker, Myles, Gudger, Byrne, Graham, Dean, G Walker, Armson, Ndlovu (Lowe 103mins), Diggin (Moyo 90mins), A Walker. Subs not used: Pitt, Cox, Farrell, Rankin, Noon.
Gillingham: Nelson, Jackson, Garmston (Wagstaff 66mins), Oshilaja, Ehmer, Hessenthaler, Herd (Wright 46mins), Knott, Dack (Donnelly 64mins), McDonald, Emmanuel-Thomas. Subs not used: Hadler, Osadebe, Pask, Byrne.
Attendance: 1,654 (93 away)
Referee: Robert Jones, Merseyside