His most prominent topics were ascension and meditation techniques. He also wrote a number of books on the topic of Spiritual Psychology, and later enhanced his publications to an "Easy-to-Read Encyclopedia of the Spiritual Path" containing numerous volumes (see Bibliography). With the growing popularity of the World Wide Web, he also composed one of the more comprehensive websites on spirituality which has often been used as a point of reference on New Age topics. Furthermore, he founded an academy for spiritual studies by the name of Melchizedek Synthesis Light Academy & Ashram (MSLA) (which then later developed into the I AM University). He served as a spokesperson for the planetary ascension movement. In this movement, his major contributions were the propagation of the concepts of "Cosmic Ascension" and "Integrated Ascension".

In the 1990s, Dr. Stone initiated the Wesak celebrations at Mount Shasta, California...annual spiritual gatherings that spawned a lot of interest in the New Age movement , but also controversy. The last Wesak celebration hosted by Dr. Stone in Mount Shasta took place in 2004 . The Wesak celebrations in Mount Shasta are still carried on today.

In 2004, Dr. Stone founded the Ascended Master Teachings organization the I AM University, a "spiritual" university to teach students how to integrate all walks of faith. In order to facilitate this, he composed a large number of study materials: 8 correspondence courses, a workbook, a 7 Year Daily planner, and a number of further resources (meditation tapes & CDs, videos, DVDs). After his passing away, the I AM University was relocated from central Coastal California near San Luis Obispo to Europe in Austria where it continues to make the legacy of Dr. Stone available to serve students of spirituality worldwide. Gloria Excelsias took over the leadership of Joshua David Stone's organization the I AM University after Stone's death in 2005. Paul McCarthy of the Sirius Temple of Ascension in Brighton, England, who channels the Sirian Masters, said in New Age thought to be a large group of beings from the planetary system of Sirius that include both humanoid and dolphinoid entities, is now also associated with the I AM University.

In the mid-1990s, Dr. Stone became the first ascended master teachings teacher ever to admit a UFO related entity, Ashtar (whom he referred to as the Master Ashtar), to the ranks of the ascended masters, by incorporating the teachings of the medium Tuella into his own teachings. Dr. Stone portrayed the "Master Ashtar" as commanding a space fleet of thousands of flying saucers watching over Earth, with the extraterrestrial being Vrillon functioning as his communications director. According to Stone, these flying saucers are based on several oblong artificial asteroids about 100 miles in diameter that function as mother ships for the flying saucer fleet, with a total population of millions of extraterrestrials, orbiting in the outer reaches of the Solar System. The saucers in Master Ashtar's flying saucer fleet are manned, he asserted, by both Venusians and aliens from the Galactic Confederation based on the artificial asteroids. According to Stone, the Master Jesus, under his "galactic" name of Sananda, works with Commander Ashtar, and is actually the Commander-in-Chief of the Ashtar Galactic Command flying saucer fleet, with his own command flying saucer. According to Stoen, another name used to denote Commander Ashtar's flying saucer fleet is The Airborne Division of the Great White Brotherhood.

Stone also pushed the boundaries of the ascended masters teachings by channeling entities dwelling farther out in our galaxy than any other medium had ever attempted to do before. He formulated a chart he called the "Cosmic Map", in which he, for the first time ever for any ascended master teachings teacher, detailed the structure of the ascended master hierarchy within the Milky Way Galaxy. According to writings of Joshua David Stone, this sector of the Milky Way Galaxy...one twelfth of the total volume of the galactic disc...is governed by a cosmic being (Elizabeth Clare Prophet's term...Stone himself uses the term cosmic master instead of cosmic being to denote ascended masters of extraterrestrial origin) named Melchior working out of the constellation of the Great Bear (Alice A. Bailey stated that each of the Seven Rays is focused from the center of the galaxy through one of the seven stars of the Big Dipper). Working with "Melchior" on the governing council of this sector of the galaxy operating from Ursa Major is said to be the [Local galactic sector] cosmic being Melchizedek (not the same being as the terrestrial Master Melchizedek, said by Elizabeth Clare Prophet to be the ascended master that the Biblical Melchizedek became after his death [ascension] on Earth). According to Joshua David Stone, there is a powerful cosmic being functioning at the galactic core of the Milky Way Galaxy named Averran, whom he identified as the governing deity of the Milky Way Galaxy and thus the personification in the ascended master teachings of what in conventional Theosophy is called the Galactic Logos. Working with Averran at the galactic core under his authority are said to be the cosmic beings Vywamus, Lenduce, Adonis and Atlanto.