A steady rain marked the second day of play and dampened the PGA Centenary Course at The Gleneagles Hotel but Scott was not at all hindered by the dreary conditions.
The 22-year-old started the day two shots off the pace on the back side but quickly began his climb up the leaderboard with a birdie at the 12th. Scott picked up two more birdies at 16 and 18 to make the turn at minus 8.
Scott continued the barrage with back-to-back birdies from the second to move to 10-under and distance himself from the field. The winner of the Qatar Masters nearly found trouble at the par-3 sixth after he missed the green off the tee but managed to get up and down to save par and keep the momentum on his side.
At the par-4 seventh, Scott knocked his approach to 20 feet and drained the putt for a birdie. He capped off his round with a four-foot birdie at the par-5 ninth for a new 36-hole tournament record.
Scott, who was excluded from this week's World Golf Championships event, was focused entirely on the challenge at hand.
'I am not here just to play, I am here to win this golf tournament and do the best I can and I'll do that wherever I am,' said Scott, a two-time winner on the European Tour. 'Obviously I would have loved to have played in Seattle but seeing I am not, I'm happy to be here and I want to win this one.'
Not everyone was as content with the conditions as Scott, including overnight leader Green.
'It was pretty miserable out there,' said Green, who managed a second round 71 to finish at 8-under-par 136. 'Everything was wet, grips were wet, hands were wet, my caddie was wet, everything. In conditions like that you just have to try and do what you can to stay as dry as possible and get around.'
A group of three were knotted at 7-under-par 137, including European Ryder Cup captain, and local favorite, Sam Torrance.
'I played very, very solidly out there,' said Torrance, who posted a four- under 68 Friday. 'I missed the fairway once. I did some good work with my dad this week. One of the main faults I have had is that I had a twist in my takeaway and this is what I have been working on.'
Torrance was joined by David Park of Wales and England's Mark Roe in a tie for fourth.
The Scottish duo of Andrew Oldcorn and Raymond Russell were part of another group one shot further back. They were joined by Ignacio Garrido, Matthew Cort, Fredrik Andersson, Philip Walton and Jeremy Robinson at 6-under-par 138.
Defending champion Paul Casey struggled with a 74 to finish at 2-over-par 146. The Englishman, who earned his maiden victory at this event last year, will play the weekend, however, as the cut fell at 3-over-par 147.
Among those who did not make the grade were 2001 U.S. Amateur winner Bubba Dickerson and 1988 Masters champion Sandy Lyle.
Full-field scores From Diageo Scottish PGA Championship