Johnson is charged with kidnapping, attempted first-degree murder and other related offenses.
Milligan, of Gaithersburg, Md., testified he had been in Frederick, Md., on Aug. 2, 1996, looking at a car to buy for his car dealership.
He stopped at the Old Town Tavern and had two or three beers before heading for home, Milligan said.
He pulled into the Sheetz convenience store and a woman, later identified as Tammy Reel, asked him for a ride to her motel.
Milligan said he followed her up to her motel room.
"I had to use the bathroom rather badly," Milligan said.
Reel, who is charged with the same offenses as Johnson, testified earlier this week for the prosecution that she lured Milligan into the Days Inn room and that Johnson attacked him from behind as part of their plan to steal a car. Reel is cooperating with authorities as part of a plea agreement.
Johnson had entered the room briefly, asking for a cigarette and asking if Reel was all right, Milligan said.
As he spoke to Reel, a large hand suddenly covered his mouth as he was attacked from behind, Milligan said.
He felt himself being choked and he slipped out of the man's grasp briefly, losing his glasses in the process, Milligan said. But the man overpowered him and he lost consciousness, he said.
When he came to, he was in the trunk of his car. He checked his watch. It was 2 a.m., Aug. 3.
Milligan said he believed he slipped in and out of consciousness.
"I remember having all sorts of thoughts about trying to make a heroic escape," Milligan said.
But he did not have his glasses, he was missing a shoe, he was bleeding and he did not know where he was.
About 7 a.m. on Aug. 3, the car stopped and he heard the man he later identified as Johnson call out for the woman to help get him out of the trunk.
Milligan said he thought it was safest to play dead. He said he wondered if it would be his last day alive.
He prayed and the trunk opened.
"My first reaction was this incredible rush of fresh air. The air in the trunk had been extremely stale," Milligan said.
He felt arms picking him up under his shoulders and he stayed as limp as possible.
Milligan said he felt himself being swung back and forth before he was released and was falling through the air.
When he felt himself land in water, he stayed under for as long as he could, about 20 seconds, Milligan said.
When he surfaced, he floated with just his face above the water, worried that they would return to make sure he was dead.
Later, after making sure they were gone, he went to a nearby campground.
Milligan later spent three days in the Jefferson Memorial Hospital with a concussion and numerous bruises.
Police testified Thursday how they gathered evidence left at the motel room and in Milligan's car, including blood on a bandage found at the motel room that matched Johnson's DNA.
Only one person in about 2 million would have a similar DNA pattern, police testified.