The Spaniard hit a five-under-par round of 67 for the second successive day at the Portstewart Golf Club to move on to -17 overall.
Rank outsiders Im and Hebert both shot rounds of 67 to lie 13 under and retain the one-shot lead they held over the chasing pack after the first round. He missed the cut.
The victor is now due a payout worth $1,166,669 of the $7,000,000 prize money, according to the European Tour's prize money distribution chart (h/t GolfNewsNet), which also details all the payouts from this tournament.
ONEIDA, Wis. - Katherine Kirk shot a 7-under 65 on Saturday to open a four-stroke lead in the Thornberry Creek LPGA Classic, and move into position to challenge the tour's 72-hole record. Notes: McIlroy is the tournament host.
Paul Dunne is best placed of the Irish contingent on eight under, along with others, including Jamie Donaldson and Soren Kjeldsen, two of 11 former Irish Open winners in the field.
McIlroy may have missed the weekend but the 92,534 souls who flocked to this week's venue got to see a player who could yet go on to be his equal take the spoils.
It was the second time in three years the defending Irish Open victor had missed the halfway cut and the fourth occasion in the past five years McIlroy will sit out the weekend rounds in the premier Irish event. He will play one more event - the Scottish Open at Dundonald Links next week - before the British Open, which starts on July 20 at Royal Birkdale.
There's major benefits for Inishowen in hosting the event, including priceless television coverage across the world and up to 90 thousand visitors to the region as experienced by Portrush and Portstewart in recent years, which leads to a vital contribution to the local economy.