The Iron forward played as his current club, locking horns with League One side Bolton Wanderers.
Despite going behind early on, McAtee drew level straight away with Yasin Ben El-Mhanni the scorer before his own character took centre stage for the remainder of the first half, notching twice to put the Iron in a 3-1 commanding lead.
The Trotters hit back with an early goal in the second half before drawing level towards the end of the game.
Scunthorpe thought they'd won it when Kevin van Veen rolled in the fourth, but in the fourth minute of two added, Bolton turned the ball home for an equaliser.
McAtee will next face Ben Wilmot of Swansea City followed by Ryan Fredericks of West Ham United, with confirmation of details to follow in due course.
In the other game, the Swans and the Hammers drew 2-2, with a similar last-gasp equaliser.
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The last tournament, which was organised by Leyton Orient, was put in place to raise money for two charities and the EFL clubs, while this competition has seen attention turn to the work of the NHS.
The tournament is raising money for NHS staff and projects to support those suffering with COVID-19. You can donate on the tournament’s Just Giving page: www.justgiving.com/fundraising/stayintertotocup