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Ebbsfleet now trail leaders Maidenhead by 11 points in National League South after a thrilling clash at Stonebridge Road.
Both sides finished with 10 men but the Fleet were never able to get going against a robust Maidenhead team.
It needed a hat-trick of headers by Sean Marks to sink the Fleet, the winner coming in the 89th minute.
The Fleet were furious when Maidenhead took an eighth-minute lead. Danny Kedwell was flagged offside but didn't touch the ball until he was in his own half - and that's where the visitors took a free-kick from.
Under the law change in the summer the free-kick is allowed to be taken where the player touches the ball - even if it is in his own half.
From the free-kick, Maidenhead worked the ball forward and after the hosts failed to clear, Marks headed in to put his team ahead.
Fleet responded in positive fashion. Darren McQueen and Anthony Cook both tested keeper Carl Pentney before they levelled on 23 minutes.
Sean Shields worked some space in the box where there seemed to be none and his low finish from an acute angle found the far corner.
But Maidenhead did not arrive at Stonebridge Road top of the league without good reason. Their well-organised approach is also added to by some glimpses of quality and Marks produced an even better header second time around from Harry Pritchard's cross to restore their advantage five minutes later.
Fleet keeper Nathan Ashmore then did well to turn over Ryan Upward's effort as Maidenhead edged a lively first half.
For the second week in a row, Fleet replaced Sam Deering at half-time as, again, boss Daryl McMahon matched up with a 4-4-2 formation.
Early bookings after the break for Maidenhead's James Hammond and James Comley underlined how they broke the game up with regular fouls to stop the Fleet getting into full flow.
McQueen headed straight at Pentney just before the hour from Danny Kedwell's excellent cross before the game took a twist on 61 minutes.
Maidenhead's Comley went in with both feet on Anthony Cook after the referee had already blown for a Fleet free-kick - and was rightly shown the red card.
Fleet started to pile on the pressure but Maidenhead showed exactly why they have the best defence in the division with a series of important blocks around their own penalty area.
It needed a moment of brilliance to get the Fleet back on level terms - and it arrived on 78 minutes. Powell picked a perfect ball into substitute Bradley Bubb, who turned his marker and fired low past Pentney.
The game took another turn in the 81st minute. An awkward, but certainly not dirty, challenge by Fleet centre-back Mark Phillips saw him see red for a foul on Marks, who was not the last man with Connors covering behind. It was a case of referee Elliott Kaye levelling things up with the red cards.
It proved a big call as Marks completed his treble in the 89th minute, heading in unmarked after a long throw-in was flicked on.
Ebbsfleet: Ashmore, Cook (John 81mins), Shields, Phillips, McCoy, Clark, Rance, Deering (Connors 46mins), Kedwell, McQueen (Bubb 61mins), Powell. Subs: Sheringham, Miles.
Maidenhead: Pentney, Hammond, Steer, Upward, Massey, Inman, Tarpey, Comley, Marks, Mulley (Barrett 84mins), Pritchard (Smith 63mins). Subs: Wassmer, Kelly.
Attendance: 1,318.