For decades, Reverend Adam A. McAlister held services in whatever room on the base could be temporarily rigged for worship -- a practice the Navy called being "rigged for church." McAlister had served as Mare Island's chaplain since 1873, and the makeshift arrangement rankled him. He was a man who could endure the Navy's bureaucratic indifference, but not forever. Eventually he leaned on his friendship with U.S. Senator George C. Perkins, convincing him to slip a $5,000 appropriation into the 1900 Naval Appropriations Act for chapel construction. Architect Albert Sutton drew up a wood-framed, one-story cruciform church on a brick foundation, oriented east to west with the sanctuary and altar at the western end. The building was largely complete by October 1901, though Sutton's full plan was not finished until 1904. McAlister had his chapel. He would spend the rest of his life filling it with memorials.

The stained glass arrived window by window over the next fifteen years, most of it donated by families of Navy personnel in memory of loved ones who had served. The Tiffany Studios pieces are the collection's crown jewels. On the right side of the sanctuary, a pastoral scene depicts the Good Shepherd, dedicated to Chaplain McAlister himself with the inscription: "To whose devotion to this Chapel the placing of many of its Memorials is due." High above the altar, a nine-foot-round Rose window shows the ascendant Christ, dedicated to those "in the U.S. Navy and Marine Corps who served on the Pacific Ocean." The final memorial window, installed in 1930, came not from Tiffany but from Cummings Studio: a Madonna and Child inspired by Nicolo Barabino's painting "The Madonna with the Olive Branch," inscribed "To the Women of the Navy and the Marine Corps." Nearly all the art glass was in place by McAlister's funeral at the chapel in 1916.

St. Peter's Chapel was more than a place of Sunday worship. For generations of Mare Island families, it marked every passage that mattered -- baptisms, weddings, funerals. The chapel's guest books read like a social history of the Pacific Fleet. During World War II, the pace of weddings accelerated sharply as young sailors married before shipping out to the Pacific Theater, uncertain whether they would return. Historian McDonald observed that "the chapel, more than any other building, bears witness to the closeness of the community that developed at the Mare Island Naval Shipyard." The commemorative tablets on the walls and ceiling accumulated alongside the windows, each one placed by parishioners and donors, each one a thread connecting the living community to its honored dead.

Mare Island Naval Shipyard shut down in 1996 after 142 years of continuous operation, the longest-serving naval shipyard on the Pacific Coast. The closure left St. Peter's Chapel stranded on a former military base transitioning to civilian use. But the building endures. Its cruciform shape remains mostly intact, altered only by a 1929 rear addition for the organ and two modest 1963 side additions that were carefully integrated into the original design. The brick foundation still supports the original wood frame. The Tiffany windows still catch the morning light. Listed as a National Historic Landmark, the chapel stands as evidence that the most lasting things built on a military base are not the dry docks or the machine shops, but the places where people gathered to mark the moments that mattered most.