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The world No 1 always faced an uphill battle to avoid a third straight cut in the event after crashing to an opening 80, with McIlroy failing to make the weekend after a second round 71 at Royal County Down GC.
McIlroy made his first gain of the round with a lengthy putt at the seventh, before keeping his slim hopes alive with a birdie at the 12th to move back within two of the projected cut.
After a five foot par-save dribbled in at the 14th, McIlroy lost his advantage with a double-bogey at the next, sending his second shot into the rough and thinning his third past the green before three-putting from 40 feet.
Birdie chances from within 10 feet at both the 16th and 17th were dragged wide of the cup, before the tournament host gave the sell-out crowd something to cheer about by rattling in a lengthy birdie at the last.
“When the wind is like this, even when you’re giving yourself birdie chances it’s hard to take them,” McIlroy told Sky Sports 4. “I was trying out there as hard as I could, but just couldn’t get a run of holes going and any momentum.
“I was a couple under through 14 but still needed a good finish, but unfortunately I wasn’t able to do that. I left myself too much to do from yesterday and felt I played a solid round of golf today but just wasn’t enough.
“The support out here is phenomenal; it’s the third year in a row that they’re not going to get to see me play over the weekend, so it’s disappointing to say the least.”
Ryder Cup team-mates Martin Kaymer, Sergio Garcia and Victor Dubuisson also failed to reach the weekend, while American star Rickie Fowler is safely through after carding a second consecutive level par 71 of the week.