In the Lions den it was Church who gave Orient hope, before an ex-O came back to haunt the visitors and snatch all three points for Millwall.
Gary Alexander, a hero of Orient's 2005-2006 promotion campaign, scored twice for the host's to cancel out Simon Church's opening strike.
But the real action started with the final whistle, with low, low farce.
Then, around 600 home fans invaded the pitch and rushed to the away end, where they taunted Orient's big travelling contingent high above in the top-tier.
There was comedy too, as a tanoy announcement warned against corner-flag theft.
Millwall at the New Den have made big efforts to dispel their controversial reputation.
But the incident spoke loudly of the fact that old habits die hard. The CCTVs on sticks at the front of the away-end to film how Lions fans treat their guests look to have been well placed.
The shameful incident finally ended with a pitch-wide row of orange-jacketed stewards and police horses marching up-field to force bonkers fans to beat a retreat.
The game had been hard for Orient, as they were forced to soak up long spells of pressure, after McGleish missed a penalty in the eighth minute.
20-year-old Church struck for the guests with the first goal of the game against the run of play, on 47 minutes.
He applied the finishing touch into the far corner past keeper David Forde from Scott McGleish's pass and before him, keeper Jamie Jones's big punt up-field. The strike silenced the noisy Lions fans and put Orient's big travelling support on cloud nine. But not for long.
Alexander, who last helped transport the fans to that level during Orient's promotion clincher three years ago, levelled the tie on 70 minutes with a thumping shot from just inside the box.
Then, in the 86th minute he applied the header at the far post from James Henry's deep cross to seal three points.
And then the action began.
Jones (GK), Purches, Mkandawire, Thornton, Morgan (booked 68), Terry, Daniels, Smith, Spence, McGleish (sub 79 Demetriou), Church (sub 69 Gray).
Subs: Morris (GK), Saah, Melligan, Gray, Demetrioiu.
Attendance: 11,414 of which: 1,101 Orient fans.
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