In 2380, he was attempting a spiritual ascension, something he claimed he had been working on for a decade. Ensign D'Vana Tendi was assigned to observe this and was the last of eight Starfleet personnel to arrive at O'Conner's quarters for the experience. In preparation, O'Connor had worked on a sand mandala for two years, but Tendi accidentally destroyed it when she dropped his Tzutchian gong into it.
After the USS Merced caused a hull breach on the ancient generation ship they were towing, some of the terraforming emulsion affected the Cerritos and began turning parts of the ship into a coral-like substance. Tendi and O'Connor were trapped in engineering, which was flooded. O'Connor confessed that his ascension was never going to happen, and that he had been faking it in an attempt to stand out from the crew. Tendi helped them both escape and O'Connor kissed Tendi before he began to levitate and began to glow as his ascension began.
During the course of his ascension, O'Connor was in pain as he was burning, stated that he could "see everything" and that "time has no meaning". He saw Abraham Lincoln, and stated that the entire universe was balanced on the back of a giant koala. His last words were "The Secret of Life is..." before vanishing as an energy being. (LD: "Moist Vessel")