McIlroy sits tied for second behind halfway leader Greg Chalmers at The Australian Golf Club in Sydney but it was Scott who made the headlines after a poor start to the tournament on Thursday.
The world No 3 carded three birdies and an eagle in his round of 66 and that was enough to move him into a tie for ninth, just three shots off the pace being set by left-hander Chalmers.
“Yesterday I got off to a bad start, and I didn’t scramble well when I had to and it started to get away from me,” Scott said. “Today a couple of good shots coming up 14 and I made an eagle and momentum is on your side.”
Chalmers, a dual winner of the event, also shot a second-round 66 which mixed in a couple of dropped shots with seven birdies and was just one worse than the best round of the day, a 65 from American Jamie Lovemark.
McIlroy played in tougher conditions in the afternoon group, and he had more than his share of problems in shooting a topsy-turvy round of 69.
The Open champion had three bogeys in his first seven holes and dropped three more shots on the way back to the clubhouse, but three birdies and an eagle in his last five saved the day.
“I felt like I had an opportunity today to maybe shoot a good one and put a little bit of space between myself and the rest of the field, but it didn’t really pan out that way,” said McIlroy, who twice found the water on his way around.
He sits in a four-way tie for second on four-under alongside Australia’s Adam Crawford, Conrad Shindler from the Unitd States and home amateur Todd Sinnott, who was one of the day’s stars with a round of 67.
First-round leader Jordan Spieth, who was in the same group as Scott, failed to take advantage of the better scoring conditions in a round of 72 that leaves him in a tie for sixth, one shot ahead of his playing partner – he had four bogeys and only saved his day with birdies at his final two holes.
“It was a struggle, big-time struggle,” Spieth said. “I wasn’t hitting it well. ??If I wasn’t putting well I may have shot 45 on the back nine.”