The two-time defending AFL premiers were walloped by and under-manned Sydney at the SCG, setting up a sudden death semi-final against Adelaide on Saturday.
McCluggage, returning from a three-week absence due to a calf injury, was one of many to have their colours lowered against the Swans.
An All-Australian last season, the co-captain has played just 14 games - winning seven - in this campaign.
Fagan dropped young defender Ty Gallop to make room for McCluggage last week, but Gallop is back in the side to face the Crows after small defender Noah Answerth (ankle) was hurt in Sydney.
McCluggage has averaged about 10 disposals (17.6) and almost five contested possessions (7.2) less this year than in his brilliant 2025 campaign.
"He's actually a champion. He's an All-Australian and been out for about six weeks, so we'll give him that game," Fagan said of McCluggage, who had 16 disposals in a season-high 81 per cent of game time played.
The coach had been critical of his side's mental application last week but said he wouldn't be able to tell if that had improved until Saturday night.
"They've done everything right this week … but at the end of the day you're judged by how you perform in the game," he said.
Ryan Lester will take a small defender in Answerth's absence, with Fagan content to reinstate Gallop alongside Harris Andrews and Darcy Gardiner to counter the Crows' tall trio of Riley Thilthorpe, Darcy Fogarty and Taylor Walker.
"We've always felt Ryan Lester can play that swingman role in defence. He can play small, he can play tall," he said.
"It'll come down to the collective and how fierce we are in the contest and how willing we are to bounce back from last week."
The winner will earn a date with Hawthorn at the MCG in a preliminary final next week.
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