It was designed by Dr. Earle L. Reynolds (1910–1998), an anthropologist who had been sent to Hiroshima by the National Academy of Sciences to research the effects of the first atomic bomb on the physical growth and development of surviving Japanese children (1951–1954).

From there they sailed to New Zealand (Auckland and Wellington); Australia (Sydney, the Great Barrier Reef, Cairns); Indonesia (Bali, Java).

The Historical Chronology of the Galapagos, 1535–2000 records in February 1958 that "The Phoenix, with Earle Reynolds, his wife Barbara, their children, Jessica and Ted and a Japanese crewmember arrived at Wreck Bay."

Convicts living in the penal colony on Isabela Island were asked to prepare a celebration on February 12 but on the 9th they revolted with stolen weapons and took the guards prisoners.

Months later, Earle read in a back issue of Life Magazine[6] that the Valinda had arrived in James Bay the night before ("while we were all asleep aboard the Phoenix, five miles away around the point") but was then hijacked by the 21 escapees from the penal colony who forced the crew to sail to Ecuador.

Its crew of Quaker pacifists, Albert Bigelow, George Willoughby, William R. Huntington, James Peck and Orion Sherwood had attempted to sail into this forbidden zone to protest nuclear testing and had been brought back by the U.S. Coast Guard.

[12] Impressed by the reasoning and character of these men, Earle and Barbara joined the Society of Friends (Quakers) and considered taking over their protest in the Phoenix.

(Years later, in private correspondence, Captain Bigelow wrote Earle that most people had never heard of the Phoenix and thought the Golden Rule had sailed into the area.)

They were intercepted 65 miles (105 km) inside the forbidden area by an American Coast Guard vessel, the Planetree, whose armed officers boarded the yacht and put Dr. Reynolds under arrest.

They ordered him to sail the Phoenix to Kwajalein, escorted by the Navy destroyer Collett and from there they flew him, with Barbara and Jessica, back to Honolulu for trial.

Barbara returned to Kwajalein to help Ted (then age 20) and Mikami sail the Phoenix back to Honolulu, a trip of 60 days (August 15 – October 14) against the wind,[13] while Earle was being tried and convicted for entering the off-limits zone.

The Phoenix was declared a Japanese national shrine, and city buses were re-routed past its dock so bus conductors could point it out to passengers.

As the Japanese government would not give Mikami a passport to travel to the Soviet Union, American citizen Tom Yoneda sailed with them.

A multi-national crew delivered nearly a ton of medical aid to the Red Cross Society of North Vietnam for victims of the war.

He and Akie sailed the Phoenix to San Francisco and settled at Quaker Center in Ben Lomond, California, near Santa Cruz with the boat moored at nearby Moss Landing.

John Gardner of Lodi, California, then 31, took possession of the Phoenix and had it towed up the Sacramento River, hoping to restore it and use it to rehabilitate young people recovering from substance abuse.