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After returning to Summers, the four enter Toto, where they procure a boat and travel to [[Scaraba]], but encounter a mighty [[Kraken]] along the way. After defeating the Kraken, they arrive in Scaraba, where they explore a pyramid in the desert and gain the Hawk Eye. Outside the Pyramid, Ness and his party encounter the [[Star Master]], who requests that Poo leave the party with him in order to learn PK Starstorm. Poo leaves, and the rest of the party discover [[Dungeon Man]], previously Brick Road. Dungeon Man briefly travels with them before becoming entangled in various trees. Despite this, however, Ness and his friends acquire a submarine within Dungeon Man and travel into the [[Deep Darkness]], a path leading them under the earth. Using the Hawk Eye, Ness is able to navigate through the Deep Darkness, where they once again encounter Master Belch, now known as [[Master Barf]]. After battling Barf, Poo suddenly reappears and finishes off Barf by unleashing PK Starstorm. With Barf defeated, they find [[Tenda Village]], a small community populated by extremely shy creatures known as [[Tenda]]. Apple Kid then calls Ness again, telling him that he is now working with Dr. Andonuts to create a machine known as the [[Phase Distorter]]. Suddenly, Apple Kid finds himself and Andonuts kidnapped by Porky, who also steals the prototype phase distorter. Returning to Winters, the group infiltrate the [[Stonehenge Base]] and battle the [[Starman Deluxe]], the overseer of the base. After defeating the Starman Deluxe, Andonuts and Apple Kid are rescued, and Apple Kid gives Ness the [[List of key items in EarthBound#Shyness book|book of overcoming shyness]].
Returning to Tenda Village, Ness gives the book to the village chief, who reads it to the entire tribe and allows all of them to overcome their shyness. This enables Ness to speak to the villagers, who allow passage to a dark, ominous cave, which contains the seventh sanctuary. The group then enters the [[Lost Underworld]]. There, they discover more Tenda and a talking Rock, who tells Ness of his destiny to unite the sanctuaries. Ness and the group then reach the final sanctuary, but Ness falls unconscious and enters a strange world composed of his dreams afterward known as,
[[Magicant#In EarthBound|Magicant ]]. There, he travels to the [[Sea of Eden]] and encounters [[Ness's Nightmare|his nightmare]], the embodiment of Ness's evil. After defeating it, Magicant vanishes, and Ness absorbs the power of all eight sanctuaries, becoming incredibly powerful before awakening.
After awakening, Ness and the group return to Saturn Valley where Dr. Andonuts, Apple Kid, and various Mr. Saturns have created a new Phase Distorter, a time traveling device. Unfortunately, however, they find that the machine does not work, as it is lacking a critical component: Zyoxinite, a rare material only found in asteroid deposits. Recalling the asteroid in Onett, Ness returns to his home, only to find the area invaded by hordes of Giygas's soldiers and its inhabitants locked in their homes. Ness makes his way through the invaded town and reclaims the meteorite, then returns to Saturn Valley to give the material to Dr. Andonuts. After upgrading the machine, Andonuts explains to the kids that the machine cannot warp them to the past in their current form, as living things cannot withstand time travel and it would likely destroy their human bodies. To remedy this problem, Andonuts proposes to them to have their souls transplanted into robotic bodies, though not without warning them that he doesn't know whether or not the process is reversible. Despite this critical warning, Ness, Paula, Jeff and Poo are willing to take the risk.