"To be back here on a attractive day, it's easy to remember last summer, of course, and what I managed to accomplish a little bit down the road there", said Stenson.
It marks the second straight missed cut for McIlroy, who suffered the same fate at the Irish Open, and his third in four events as he continues to struggle in a year blighted by injury problems.
As many as six players follow in a tie for second - the most notable of which is World No 10 Rickie Fowler, one of the Americans in the field this week as preparation for next week's Open Championship.
"Anything that comes my way from here would be a bonus", said Harrington, who has played just nine events in 2017 and underwent surgery on a trapped nerve in his neck in March.
With little wind protecting Dundonald Links, McIlroy encountered benign conditions in his bid to make up for an opening-round 74 in the British Open warmup but still came up short. He thinned his tee shot right at No. 8 his second-to-last hole using a rescue club, only to pull off a superb approach from the thick rough and salvage a par from 10 feet. He made five birdies during a six-hole stretch from the first to rocket up the leaderboard.
"I haven't been able to put two rounds together, never mind four", said Ilonen, who wasn't getting carried away. So new irons in the bag, 718s.
Starting from the tenth, Ilonen birdied the 14th and 15th before catching first after the turn.
Ireland's Padraig Harrington, German Alexander Knappe and England's Callum Shinkwin shared the lead on nine under par after two rounds of the Scottish Open at Dundonald Links on Friday. It was found by a scorer in an unplayable lie, so Harrington took a penalty drop, hacked out and made the putt.
The three-times major champion successfully defended his Open title there in 2008, the last time the tournament was played at the venue.
McIlroy is a three-time runner-up (2009, 2011, 2014) in the Alfred Dunhill Links Championship, was T3 in the 2010 Open at St. Andrews and also posted T5 in last year's Open Championship at nearby Royal Troon.
From 4 over after four holes, McIlroy recovered to 1 over after 16, with three of his four birdies coming via tap-ins on par fives.