Chalmers matched Scott's five-under 66 in the more difficult afternoon conditions to hold the outright lead at the 36-hole mark.
World number one McIlroy played in the group behind Chalmers and kept the large galleries entertained with a roller-coaster round of two-under 69 that included an eagle, six birdies and six eagles.
"I actually think I played much better than I played yesterday so I don't quite feel like the score reflected, but very happy with my game and that's a good sign going into the weekend," McIlroy said.
"I got one par in the last 10 holes but definitely that eagle on 14 was nice to cancel out the two bogeys on 12 and 13 and then the way I finished, yeah, it definitely makes me feel a bit better about my round at the end of the day."
Adam Crawford (69), amateur Todd Sinnot (67) and Conrad Shindler (68) share second spot, one clear of three players including overnight leader Jordan Spieth who battled to a one-over 72 in the morning wave.
"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."
Scott took full advantage of the benign morning conditions, storming from a share of 82nd spot to within three of the lead.
The world number three started the day at three-over par and in a share of 82nd spot after an opening 74 on Thursday.
An eagle at the par-five 14th sparked the Queenslander who added three birdies in his blemish-free round.
Scott's 66 was the course record for around 20 minutes before American Jamie Lovemark went one better with a six-under 65 to get back to level par.
"We had a good morning for it this morning, so I had to take advantage just for the sake of getting myself back into the tournament," Scott said.
"Momentum is a big thing ... I scrambled well and then all of a sudden a couple of good shots down 14, I make an eagle and momentum's on your side then.
"I tried to keep that rolling today and I needed to because it was the only chance I had to kind of be in touch with the lead."
Chalmers holding McIlroy at bay, Scott lurking
