McIlroy will have Manassero for company in the final round after the Italian mixed three birdies and four bogeys in a 70.
Manassero, who ended an 11-year wait for a DP World Tour win earlier this year in South Africa, had three bogeys in a five-hole stretch on his front nine, and while he birdied the par-five 12th, he let another shot slip after finding the gorse with his drive on the 17th.
Still a factor is MacIntyre, who thrives in blustery conditions and has already won twice on the PGA Tour this year.
The 28-year-old Scot was four-over through seven holes of his second round before turning things around in spectacular fashion with a run of five straight birdies to move to one-under at the halfway mark.
And by improving his score by two on Saturday, he will be fancied to make a move on Sunday and tear up the script for McIlroy as he bids to become the first player to win the Scottish and Irish Opens in the same season.
“I thought it was brilliant from kind of start to finish there,” said MacIntyre, who was pipped to the 2023 Scottish Open title by McIlroy.
“It was absolutely brutal. Even downwind, you think you’re going to get a bit of respite but it’s so hard to control the golf ball. It feels like there’s a disaster around the corner at any moment.”
Hojgaard remains a factor, too, the Dane’s cause aided by three successive birdies to start his back nine as he joined the group on three-under alongside MacIntyre, England’s Jordan Smith (69) and South Africa’s Erik van Rooyen (71).