The first Phase Distorter is stolen by Pokey Minch before Ness and friends have a chance to use it. Andonuts and the Apple Kid have to construct another Phase Distorter, called the Phase Distorter, version 769. The second Phase Distorter takes on the appearance of a Mr. Saturn and requires Zexonyte to operate.
After Ness and his friends use the upgraded Phase Distorter to travel to an unreachable part of a cave (is titled The Cave of the Present) in the Lost Underworld, they find a Mr. Saturn who reveals that Pokey escaped to the past. Dr. Andonuts, Apple Kid and another Mr. Saturn arrive in a third Phase Distorter, the Phase Distorter 3, and tells the children that using the Phase Distorter 3, they can travel to the past and pursue Pokey, but that Ness and friends must have their souls transmitted into robotic bodies before using the invention, as time travel would likely destroy their human bodies. Once the Phase Distorter 3 is used and Ness and friends arrive at their destination, it can be used to repair the robot bodies and call Ness's father. Once they arrived in The Cave of Past, they can no longer go back in the present timeline.
The Phase Distorter later makes a cameo appearance in Mother 3. It is on display in the Empire Porky Building's Hall of Memories. However, it cannot be used, and is only seen by Lucas and co. as their boat drifts by its pedestal.
During Leder's story of how Tazmily Village came to be, he mentions that Porky used a "Time Distorter" to travel through time and space at will, and bring the Pigmasks - along with Dr. Andonuts and people from several other eras - to the Nowhere Islands. It is unknown if the Phase Distorter in the Hall of Memories is the specific machine in question.