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The identity and true nature of the man referred to as "The Observer" is not known. His presence has been documented at the scene of numerous Fringe phenomena, but he observes rather than acts. He writes down all of his observations in a black notebook. He also has a fondness for spicy food, and drinks plain water. He appears to share a telepathic bond with a young proto-Observer (in "Inner Child"), but the origins of his own abilities, if any are not known. He and Walter Bishop are on speaking terms, and Walter appears to know who and what he is. He may or may not be gathering information for the alternate universe: a courier turns over gathered information on this reality to the Observer, or someone looking like the Observer, for delivery to "the enemy" in "Fracture."

William Bell is Walter Bishop's partner and fellow scientist. The two men worked together at Harvard in the 1960s and conducted a series of "Fringe" experiments on individuals. As has subsequently been revealed, Bell at least was aware that they were breeding soldiers as part of a defensive action to protect the "home" reality from invasion and/or destruction by New Wave soldiers from a parallel universe. While Walter was committed to an insane asylum, Bell patented their research and used the proceeds to create Massive Dynamic, a high-tech development company. At some undetermined point, he transitioned over to the parallel universe where he occupies an office in one of the World Trade towers, which remain intact in that reality. He is able to bring certain individuals from one reality to another, although the process is fatal unless the individual has certain unique abilities (such as Olivia Dunham, one of his test subjects). Bell remains dedicated to protecting his home reality, although his methods are often oblique. He appears to be in ill health, given his use of a respirator in the alternate reality. Alternately, it may be some side effect of living in a different reality than his own.