Well that was not in the script.
This was the stuff of nightmares for the Gunners. All with an open goal miss at the death from the skipper to add to the agony.
An away win in Piraeus really shouild have been the stepping-stone to a routine victory, with the home leg to come at the Emirates.
But the Gunnners sleep-walked their way through Thursday evening's second leg - seemingly anaesthetised by the ranks of Olympiacos players who were massed behind the ball all night.
Instead of trying to speed up their approach to get behind the stubborn Greek defence, they opted to pass sideways. Slowly. And often. Repeatedly.
Where was the urgency they needed?
Arguably, only the industrious Nicolas Pepe appeared to have the wherewithall to breaK the visitors. He at least was willing to take on players and try to make things happen.
Considering Mikel Arteta has identified the Europa League as the only realistic means of guaranteeing a return to Champions League football next season, this was a bafflingly anaemic performance from the Gunners.
And where was the marking in the 53rd minute when defender Pape Abou Cisse was allowed to venture up for a corner and head home, unimpeded, to make the aggregates score 1-1 and send the game into extra time?
Olympiacos, to be fair, gave Spurs a run for the money in the Champions League group stages, drawing 2-2 in Greece and giving Tottenham a brief scare before losing the return 4-2.
And they managed to frustrate Arsenal until the 113th minute, when Pierre-Emerick Aubameyang's acrobatic finish finally seemed to have ended the torment.
In the event, there was to be even more despair on the horizon, as Youssef El Arabi turned in a cross from the right a minute from time to send the Greeks through on away goals.
The pandemonium on the Greek bench as they raced towards their heros, realising they had pulled off a stunning victory, was entirely understandable. This is one they won't forget.
Alas for Arsenal, it is in keeping with a competition that turned nasty on them in Baku in last season's final and they found a devilish way to suffer again.
But what a missed chance at the death from Aubameyang. A miss with the goal at his mercy will haunt him - and Arsenal's season.