After setting a new course record of a seven under par 64 in the first round, McIlroy returned to the stunning Aberdeen links where he stumbled his way to a seven over par 78, dropping back to a share of 34th place at level par.
Three players - Sweden's Kristoffer Broberg (71), Scotland's Marc Warren (69) and Argentina's Ricardo Gonzalez (71) - share the lead on six under par.
However the 44-year old Gonzalez, and a four-time European Tour winner, had to call a penalty shot on himself when he found bushes down the final fairway and when leading by two shots.
Gonzalez eventually walked off with a double bogey as he looks to a first win in four years.
McIlroy had confirmed his status as British Open favourite on the opening day in muscling his way to a one stroke lead at his first Scottish Open since 2009.
However, on Friday in bright but windy conditions, he carded just one birdie at the sixth with six bogeys and a 12th hole double-bogey where he found a greenside bunker and took two shots to find the green.
"I would be happier standing here after shooting a couple of 71s but that's not the case," he said.
"It hasn't been case all year that I've got off to great start and just fell away because I am still in the tournament and can go out there in the morning and get a few of those shots back I lost.
"And this Friday thing and having to talk about it, as it's always being brought up. It's sort of in my mind and maybe I put myself under even more pressure and instead just get off to a decent start and shoot a good score.
"So it's another Friday out of the way, and I can go onto the weekend."
Broberg's recent good form continues as he looks to win for a first time on the main Tour after winning four times in 2012 on the secondary Challenge Tour.
However the 27-year old Stockholm golfer was also counting the cost of a 14th hole double-bogey when also leading at eight under par.
"I again had to stay very patient out there as it's very tough with the back nine brutal as we saw when I took the double on 14," he said.
Warren is determined to make amends for letting victory slip in the 2012 Scottish Open after leading at Castle Stuart with eight holes to play but then missing out on the eventual play-off by a shot.
"What happened two years ago was tough to swallow, but it was good experience, and I think in the future will stand me in good stead," said the Scot.
Defending champion Phil Mickelson was headed to the nearby and two-year old Trump International Links Course Scotland to practice after his round of 73 for a share of 19th place on one under par.
Missing the two over par cut-off mark was American Kevin Stadler who shot a 71 for a three over par tally, less than a week after letting slip victory in the French Open.
Also at three over par was former world and European No 1 Lee Westwood (73) along with six-time major winner Nick Faldo who was two under par after six holes but slumped also to a 73 and a four over par total.
Leading second round scores at the Scottish Open hosted by the par-71 Royal Aberdeen Golf Club on Friday:
136 - Kristoffer Broberg (SWE) 65-71, Ricardo Gonzalez (ARG) 65-71, Marc Warren (SCO) 67-69
137 - Justin Rose (ENG) 69-68
138 - David Howell (ENG) 68-70
139 - Lucas Bjerregaard (DEN) 70-69, Mikko Ilonen (FIN) 71-68
140 - Rafa Cabrera-Bello (ESP) 72-68, Fabrizio Zanotti (PAR) 70-70, Tommy Fleetwood (SCO) 70-70, Greig Hutcheon (SCO) 70-70, Shane Lowry (IRL) 72-68, Tyrrell Hatton (ENG) 69-71, Adrian Otaegui (ESP) 71-69, Michael Hoey (NIR) 66-74, Paul Casey (ENG) 69-71, Soren Kjeldsen (DEN) 70-70
141 - Mark Foster (ENG) 71-70, Paul Waring (ENG) 75-66, Matteo Manassero (ITA) 69-72, Scott Jamieson (SCO) 74-67, Stephen Gallacher (SCO) 72-69, Ollie Schniederjans (USA) 71-70, Danny Willett (ENG) 70-71, Jeev Milkha Singh (IND) 70-71, Thomas Aiken (RSA) 71-70, Tom Lewis (ENG) 70-71, Craig Lee (SCO) 72-69, Simon Khan (ENG) 70-71, Phil Mickelson (USA) 68-73, Jimmy Walker (USA) 71-70 Richard Bland (ENG) 71-70