Samuel Kenneth McDonough was arrested by a SWAT team that boarded a Victoria Clipper seven hours after it motored away and drifted in Elliott Bay on Sunday.
McDonough, 33, was jailed for investigation of burglary, reckless endangerment and malicious mischief.
Prosecutors are asking for a high bail at a Monday afternoon hearing to hold him until charges are filed, said Dan Donohoe, a spokesman for the King County prosecutor's office.
Many are wondering how the ferry was pirated away in what could have done severe damage to other boats and the bay itself. The 480-ton boat had 1,300 gallons of diesel on board.
"We were very, very fortunate this individual did not run into a state ferry or grain ship out by the grain terminal," Clipper Vacations CEO Darrell Bryan said Monday. "It was a hell of a wake-up call."
Bryan says the intruder apparently climbed through a gap over an 8-foot chain link fence to enter Pier 69, where Clipper ships make daily runs from Seattle to Victoria, B. C. Victoria Clipper is popular with tourists and ferries about 300,000 passengers a year.
He somehow boarded one of three Clipper ships and started the engine on the 132-foot catamaran. He untied a couple of ropes but broke or damaged two cleats — metal fittings used to tie ships down — to clear the dock.
"We think the guy knew enough to get going but not enough to handle the hand controls," Bryan said.
Bryan had arrived early for a meeting with captains and noticed one of his ships drifting away. He called the Coast Guard, and Seattle police and Port of Seattle police also responded. Negotiators tried for hours to talk the man into surrendering, but eventually the SWAT team boarded the ferry.
A bomb-sniffing dog checked the vessel before it was returned.
The man had taken a laptop computer from the wheelhouse and perfume from an on-board duty-free shop, Bryan said.
The company is reviewing its security with the help of a maritime consultant and also talking about the incident with the Coast Guard, Bryan said. Port of Seattle police are also investigating.
Barbed wire has already been strung through the gap that the skinny intruder crawled through, Bryan said. It's unclear how he started the engines.
"This should never have occurred," he said. "He shouldn't have been able to get into the wheelhouse. It's supposed to be locked."
McDonough was convicted of indecent exposure in 2005, 2008 and 2012, said Department of Corrections spokeswoman Norah West. He's on a GPS monitor, which is how many homeless sex offenders are tracked.
He had been jailed for violating conditions and was released on Wednesday and outfitted with a new GPS device.
McDonough told police he wanted to cross the bay to West Seattle.
"We would have preferred he found another means," Bryan said.
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