McIlroy, who completed a career Grand Slam of major titles at the US Masters in April, had been among the leaders overnight but fell to six-under as fog disrupted the entire day's play.
The world number two was out-of-sorts after a long delay. Three bogeys in his eight completed holes left him trailing England's Matt Fitzpatrick and American Michael Thorbjornsen who were both on 11-under par when play was suspended for the night.
Fitzpatrick made a strong start with four birdies in seven holes lifting him to 12-under-par.
A bogey immediately followed on eight, which was to be the Englishman's final hole of the day.
Thorbjornsen hit five birdies in 13 holes.
Johnny Keefer was the clubhouse leader at 10-under. He was tied with fellow Americans Wyndham Clark, Chris Gotterup and Kevin Roy, Australian Min Woo Lee and English overnight co-leader Jordan Smith, who all had holes still to complete.
Keefer had a single dropped shot and seven birdies in his 64.
U.S. Open champion Clark made four birdies in his 15 holes, with defending champion Gotterup chalking up three in his ten.
The event at the Renaissance Club in North Berwick, east of Edinburgh is played on a links -- or coastal course -- as is the British Open.
The 154th edition of golf's oldest major championship takes place next week at Royal Birkdale near Liverpool.