Last-gasp agony at Sixfields as AFC Wimbledon knock Cobblers out of Carabao Cup
Town were the better side for large portions of the contest and would have fancied their chances in a penalty shoot-out, but Hartigan's long-range strike deep into stoppage-time deceived Jonny Maxted and sent Wimbledon into the third round.
Cobblers showed plenty of promise in an entertaining first-half despite creating little, and they were even better in the second 45 minutes, carving out two clear chances for Dylan Connolly and Danny Rose.
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Hide AdBut it was not to be and they did not even get the opportunity to win the tie on penalties thanks to Hartigan's last-gasp winner.
Maxted, Jordan Flores, Ali Koiki and Rose were among those to return to Town's starting line-up as manager Jon Brady made six changes.
Cobblers started off with plenty of energy and intensity but there was nothing to worry either goalkeeper until the 16th minute.
That was when the game's first big chance arrived as Wimbledon worked the ball nicely down their right side before cutting it back to Dapo Mebude, who was denied by a combination of Fraser Horsfall's last-ditch block and the body of Maxted.
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Hide AdCobblers were unable to create many chances themselves but they did have a number of promising moments in the first-half with Kion Etete relentless in his pressing and hassling of Wimbledon's defence.
The only other shot of note during the opening 45 minutes came via Hartigan, who sliced a yard or two wide from long-range.
Cobblers were so nearly in on goal within minutes of the restart when Horsfall's hopeful ball forward turned into a great pass, but neither Etete nor Koiki could get a shot away.
Connolly, despite looking suspiciously offside, then had Town's best opening of the game, slipped through on goal but Nikola Tzanev read his intentions smartly and made the save.
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Hide AdAnother good chance then arrived just past the hour when Aaron McGowan, who enjoyed an excellent game, did well to keep the ball alive and find Rose in the box, but Tzanev saved well again before Etete's follow-up was smuggled off the line.
Cobblers appeared the more likely side to win but the tie looked destined for penalties as the board went up to signal four added minutes - that was until Hartigan struck in the last of those, his long-range effort somehow squirming through the body of Maxted.
Match facts
Cobblers: Maxted, McGowan, Horsfall, Guthrie, Mills (c), Connolly (Hoskins 76), Flores (Pinnock 66), Lewis, Koiki, Rose (Ashley-Seal 82), Etete
Subs not used: Roberts, Harriman, Nelson, Pollock
Wimbledon: Tzanev, Csoka, Heneghan (c), Marsh, Hartigan, Rudoni, Mebude (McCormick 73), Guinness-Walker (Lawrence 63), Pressley (Palmer 73), Kalambayi, Osew
Subs not used: Woodyard, Nightingale, Chislett, Oulah
Referee: Ross Joyce
Attendance: 3,257
Wimbledon fans: 302