Shane Lowry, who won the Irish Open as an amateur in 2009, holed from 35 feet for another birdie on the 10th to move two shots clear of the field.
A similar cheer also greeted McIlroy's tee shot finding the fairway on the first, the four-time major winner having run up a quadruple-bogey eighth on the same hole on Thursday.
McIlroy had to settle for par on the first and par-five second to remain eight over.
Darren Clarke and Graeme McDowell are both just above the cut mark on 1-over par.
James Sugrue and Padraig Harrington are 2-over.
Shane Lowry almost chipped in for an eagle on the short par-four fifth, the tap-in birdie taking him into a tie for the lead with Holmes.
Holmes, who won the Genesis Open in February but has also missed nine cuts in 16 events this season, had put the finishing touches to a second round of 68 to replace Fleetwood as the clubhouse leader.
Lowry was undeterred by the worsening conditions and another superb iron shot to the eighth set up a fifth birdie of the day.
That took the 32-year-old into the outright lead on nine under par with Rose finishing six under following a 67.
Fleetwood also had company on seven under as compatriot Lee Westwood, aided by a birdie from 50 feet on the 16th, completed a bogey-free 67.
The first of the Irish players on the Portrush Links were Darren Clarke and James Sugrue, The amateur champion Sugrue is one under with Clarke level
Padraig Harrington has picked up a shot today, he's three over, Graeme McDowell is on two over, close to the projected cut line.
While Rory McIlroy has a mountain to climb to make the cut after an eight over par first round. He tees off after 3pm.
Tiger Woods is rallying to make the cut, now four over par through 13 holes after picking up four birdies so far today.