Six months after the American Civil War began, the North was faced with a dilemma.  It was apparent by this time that the war would be neither short nor decisive; battles were being fought and large numbers of prisoners captured, but facilities for incarcerating these prisoners were lacking.  To help alleviate the problem, Lieutenant Colonel William Hoffman, Commissary General of Prisoners for the United States, was authorized on October 3, 1861 to investigate the Lake Erie Islands as a possible site for a new prisoner of war camp.

Hoffman visited all of the Lake Erie Islands, and serious consideration was given to South Bass, Middle Bass and Kelley's Islands.  All were suitable, but the nearness of Canada to the outer islands was considered to be a potential problem.  In the end, Hoffman selected Johnson's Island.  Better protected from the elements inside Sandusky Bay, Johnson's Island was also closer to necessary facilities offered by the nearby city of Sandusky.  Moreover, being the southernmost of the islands, Johnson's Island was considered to be far enough away to inhibit potential escape attempts to Canada.

Comprising 300 acres altogether, half of Johnson's Island was leased to the government for $500 a year, with the lessee also having control over the other half to prevent unwanted intrusion.  Construction was begun on a 40-acre plot on the south side of the island in November, 1861.  The camp was ready to receive prisoners on March 12, 1862.  When it finally reached full operation, the camp included more than 100 buildings, with the prison proper encompassing 13 two-story prisoner barracks located on 15 acres.  The largest of the barracks was 130 feet long and 24 feet wide; its 22 rooms could house approximately 150 prisoners.

On April 10, 1862 the first prisoners arrived, 200 Confederates transferred by special train from Camp Chase in Columbus, Ohio.  Over the next three years more than 15,000 men were to be incarcerated on Johnson's Island, the maximum number at any one time reaching 2,800 in early 1865.  The vast majority of the prisoners were Confederate officers, but a number of Confederate enlisted men, political prisoners, spies, and northern deserters were also sent to the Johnson's Island.  More than 200 would never leave.

The camp was initially garrisoned by 100 locally recruited militia called the Hoffman Battalion, named for the founder of the prison.  However, as the war progressed and rumors of escape attempts and conspiracies mounted, two forts were built to protect the prison, and at one point an earthwork housing a battery of four field artillery pieces was situated on nearby Cedar Point.  The prison garrison was strengthened at various times with a variety of units, and during one escape scare almost 1,500 troops were camped in the vicinity.

Without doubt the most notable event in the prison's history was the infamous "Lake Erie Conspiracy."  In August 1864, Charles H. Cole, a captain in the Confederate Army and later a lieutenant in the Navy, checked into a Sandusky hotel posing as an oil company employee from Harrisburg, Pennsylvania.  He was soon joined by John Yeats Beall (pronounced Bell), also in the Confederate Navy.  Together they planned and organized a mass prisoner escape from Johnson's Island.  Cole remained in Sandusky to coordinate the event while Beall traveled to Windsor to locate men, secure arms, and set the operation in motion.

The escape plan was put into action on the morning of September 19, 1864.  A portion of the conspirators, led by Beall, boarded the small steamer Philo Parsons at Detroit, Michigan as it prepared for its regular journey to Sandusky via the Lake Erie Islands.  Several more of Beall's men boarded the Philo Parsons after Beall persuaded the steamer's captain to make an unscheduled stop at Amherstburg, on the Canadian side of the Detroit River.  Altogether, Beall had managed to slip 30 men on board the little sidewheeler.  From Amherstburg the ship made its regular stops at North, South, and Middle Bass Islands, and also at Kelley's Island.  Just after leaving Kelley's Island the conspirators overpowered the crew and took control of the Philo Parsons.  As per the plan, the steamer remained on course for Sandusky Bay until, at 5:00 P.M., the conspirators observed the U.S. Gunboat Michigan, 14 guns, anchored near Johnson's Island.  The stratagem now called for the Michigan to be boarded and captured, and the prisoners on the island to be released.

Here is where the plot went awry.  Beall was informed that there was insufficient fuel to carry out the entire plan, so he decided to return to Middle Bass Island to take on more wood.  Approaching Middle Bass, the conspirators encountered another vessel, the small steamer Island Queen.  The Island Queen was seized and her stunned passengers and crew were put ashore on Middle Bass Island.  After filling the Philo Parson's wood bunkers, Beall and his cohorts again set out for Sandusky Bay, towing the Island Queen astern.  About half way to Kelley's Island, Beall opened the Island Queen's sea valve and set the captured vessel adrift.  The Island Queen eventually settled to the bottom near Chicanolee Reef, just south of Pelee Island.

As the Philo Parsons steamed toward the entrance to Sandusky Bay, the escape plan was once again aborted.  The reasons are still unknown; perhaps some additional information that Beall was hoping to receive did not arrive, or possibly a signal that he was expecting from Sandusky was never sent.  Whatever the case, the conspirators became suspicious and abandoned the attempt.  As it turned out, Beall made a wise decision.  A few days earlier a Confederate deserter had informed the military commander at Detroit about the plot, and this officer notified Johnson's Island and the Michigan's captain.  The eventual outcome, had Beall actually sailed into Sandusky Bay, can only be a matter for speculation, but with the Michigan's crew ready and waiting and the island's defenses placed on alert, Beall's plot would have had little likelihood of success.

After turning back, Beall set a course for Canada, where the conspirators scattered after making landfall at Sandwich on September 20.  Charles H. Cole, his bags packed for a trip to Toronto, was arrested that same day in Sandusky.  Tried and convicted for conspiracy, Cole spent a little over a year in prison before being released on February 10, 1866.  John Yeats Beall was captured near Niagara Falls, New York on December 16, 1864 after a failed attempt to derail a train near Buffalo.  Tried for piracy and spying, he was convicted and sentenced to hang.  Beall was executed at Governor's Island, New York on March 24, 1865.

The Civil War ended on April 9, 1865, and the government ordered that Johnson's Island be abandoned on June 8, 1865.  Years passed before the island saw further activity.  A farmer planted peach and apple trees over the prison site after the war, but an attempt to turn Johnson's Island into a resort area in 1897 was a failure.  A small village, established in 1901, was abandoned in 1908.  Later, a quarry was operated on that portion of the island which contained structures housing Union troops.  In 1905 the prison cemetery was acquired by the Daughters of the Confederacy, and on June 8, 1910 a monument was erected to the memory of the Confederate dead.  Control of the cemetery was turned over to the government in 1932, and the U.S. Department of Veterans Affairs now administers the site and cares for the 206 graves.

Over the years, both year-round and seasonal homes have been built on Johnson's Island, especially around its perimeter.  A causeway and bridge now connect the Johnson's Island to Marblehead Peninsula; the island is accessible to the public for a small fee.  As of 1996, plans were being implemented to develop additional shoreline property for residential and recreational use.