World number three Xander Schauffele fired a nine-under par 62 Thursday at Valhalla to match the lowest major round in history and was second, two back of Morikawa, when he teed off in round two.
Morikawa, who reeled off two sets of three birdies in a row in a 66 on Thursday, went two better to overtake fellow American Schauffele for the lead and reach 12-under with one hole to play.
Morikawa, ranked 13th in the world, began on the back nine and sank a 12-foot birdie putt at the 13th and a three-footer to birdie the par-5 18th.
He unleashed another hat trick starting with a birdie putt from just outside eight feet at the fourth. Next came a 17-footer for birdie at the fifth and then he holed out from just inside 34 feet at the sixth.
At the par-5 seventh and par-3 eighth, he sank birdie putt from about five feet, stretching his lead to three on 12-under.
Morikawa won the 2020 PGA Championship and 2021 British Open and comes off a career-best share of third at last month's Masters.
Scheffler, however, was the focus of most spectators, as they lined the course to cheer him every hole, some while wearing T-shirts with his new mugshot image taken hours earlier.
Scheffler, who won his second Masters title last month, shook off his arrest and booking to make five birdies against a lone bogey to share third on 8-under overall after 14 holes.
Before dawn, Scheffler was taken into custody and charged with assault of a police officer, criminal mischief, reckless driving and disregarding signals from an officer directing traffic from an incident at the entrance to Valhalla.
He was handcuffed and taken into custody after driving over a curb trying to get around a traffic accident, one that resulted in the death of a pedestrian, and according to police dragging a police officer with his car so severely the man was hospitalized.
In a surreal morning at a major for a world number one, Scheffler was ordered out of his car, arrested, booked, had his mugshot taken in an orange jumpsuit and released into his own custody just in time to get back to the course and practice before his second round began.
"This morning, I was proceeding as directed by police officers," Scheffler said. "It was a very chaotic situation, understandably so considering the tragic accident that had occurred earlier, and there was a big misunderstanding of what I thought I was being asked to do.
"I never intended to disregard any of the instructions.
"I'm hopeful to put this to the side and focus on golf today. Of course, all of us involved in the tournament express our deepest sympathies to the family of the man who passed away in the earlier accident this morning. It truly puts everything into perspective."
That accident delayed the start by 80 minutes and ensured the second round would not be completed until Saturday on a damp, receptive course.
Scheffler, a new father after his son arrived last week, hit his opening tee shot into the right rough at the par-5 10th hole but dropped his approach three feet from the hole and tapped in for birdie.
He missed the green and a five-foot par putt to bogey the par-3 11th but responded with his longest made putt of the week, a 26-foot birdie, at 12 to reach 5-under.
Scheffler left himself a birdie putt from just inside six feet at the par-5 18th and sank it, then added birdie putts from six feet at the second hole and three feet at the fourth.
Soderberg aces eight
Sharing third on 8-under with Scheffler was world number 81 Mark Hubbard, making only his fourth major start.
Hubbard birdied the par-5 10th and par-4 12th to start his round then sank a seven-foot birdie putt at the par-5 18th.
The 34-year-old American, whose best PGA Tour finish in 214 career starts was a share of second at the 2019 Houston Open.
Sweden's Sebastian Soderberg, making only his third major start, aced the 173-yard par-3 eighth hole.
