McIlroy added a 65 to his opening 68 with some scintillating play at the Club de Golf Chapultepec including a hole out for eagle at the par-4 14th.
But while the World Number Three is showing signs of his best form, Adam Scott is heading the other direction after a frustrating 5-over 76 which included a number of missed short putts.
Scott’s Strokes Gained Putting statistic, a measure of his form versus the rest of the field, is a worrying -3.976 through two rounds meaning he is giving up almost four shots per round to his peers.
Scott started his Friday round at the 10th hole where he missed an 8-foot putt for par. He missed from the same range two holes later for par again then reeled off six straight pars to go to the turn 1-over.
But his back nine was far from an enjoyable experience with a miss from three feet for par at the 4th and another from four feet, again for par, at the 6th.
He also dropped shots at the 5th and 8th and at 7-over for the week is an insurmountable 16 shots from the lead.
McIlroy, though, could hardly be in a better frame of mind as he shows some vintage form in his first tournament since fracturing a rib in January.
A balky putter has been a concern for McIlroy in recent times but there was little sign of that Friday in Mexico as he put on a clinic at the tricky host layout.
The four-time major winner went to the turn in 4-under before dropping the first of two shots of the day at the 12th.
He hit back immediately with an all-world 7-iron to 11 feet at the par-3 13th and holed the putt then set the crowds roaring when he holed a 130 metre 9-iron at the next.
Another birdie at 15 and it looked as though he might run away with the tournament but he lost momentum with a three putt bogey at the par-3 17th and a missed 3 foot putt for birdie at the last.
His eventual 6-under 65 has him 9-under for the week and two ahead of Mickelson and England’s Ross Fisher.
With 48 of the world’s top 50 in the field, though, McIlroy won’t have things all his own way over the closing 36 holes as veteran Phil Mickelson leads a strong chasing pack including the in-form Justin Thomas and World Number One Dustin Johnson.
Johnson had a horror day with the putter in round one missing five times from inside five feet but improved on day two with six birdies against two bogeys to sign for a 67 and be T4 with 36 holes remaining.
Thomas is at the same mark as is another impressive youngster, Daniel Berger, who is 6-under after an impressive Friday 66.
Marcus Fraser is the best of the six Australasians in the field after a 1-under 70 moved him to 1-under for the week.
Despite a disappointing three putt bogey at his final hole of the day Sam Brazel signed for a 3-under 68 to move 21 places up the leaderboard and be T40.
New Zealand’s Mike Hendry is T48 after a 3-over 74while Scott Hend followed an opening 5-over 76 with an even par 71 to be T60.
Adam Scott is one further back and Matt Griffin, playing his first ever WGC tournament, is last of the Australians at T75 after rounds of 78-77.
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