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To address the flaws in the EMH Mark I, Dr. Zimmerman began work on the Mark II, a prototype of which was finished in time to be included in the sickbay of the USS Prometheus in 2374.

While the Mark I's outward appearance was a copy of its inventor, a disillusioned Dr. Zimmerman changed the outward appearance of the Mark II. Furthermore, the patterns of behavior of the following versions were designed to be more pleasant and courteous and their outward appearance was changed. To achieve this, Zimmerman initially tried to improve on the programming of the Mark I, but eventually decided to create the Mark II from scratch. In addition to that, new ship designs like the USS Prometheus enabled full mobility for the EMH, as the whole ship was outfitted with holographic projectors.

By 2377, the Mark II had been replaced by a Mark III, followed by a Mark IV.

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