Even after being confronted by the real Elric brothers, the two imposter siblings continued their research on the Philosopher's Stone. However, in order to refine the Philosopher's Stone from the red water, an impatient Magwar orders that the two imposters use a different method to do so. The two refuse and quickly find themselves within an underground prison...
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Ed, Al, and the two imposters are interrupted by the guards who have heard sounds comming from inside the house. Begged to leave by an injured Fletcher, Ed and Al escape. In the meantime, Russel heals Fletcher's wounds using the stone.
Entering the ransacked room, Magwar is concerned with the security of the stone. Needing the stone finished soon, Magwar asks the two brothers to use "that" method. Suddenly, he drops the stone into a pot of red water and manipulates the wood to ensnare the two brothers. Magwar then reveals that he has known that the two brothers are Nash Tringham's sons all along.
When Ed and Al return home, they are met by Mr. Vercio and hear Elisa's coughing. Sitting by the fireplace, Vercio also makes the connection that the two imposters at the mansion are Nash's sons.
Nash was the one who discovered the red water. He went to Central city to study it, but when he came back, he said he would never research the water again or ever go back to Central City. However, Magwar drew Nash back into a life of research and the red water. As a result, the city began to prosper again; the downside was that people of the town began to develop coughs.
During their conversation, Ed and Al also learn of a Dr. Marco, an alchemist doctor, who came to the town and saved Elisa's life.
When Vercio asked about the research Nash was doing and the coughing epidemic, Nash remained reticent and left the city.
Nash's sons have been imprisoned by Magwar, and Fletcher learns of the cruel method of crystallizing the red water. By making pregnant women drink the red water, the red water will flow into the placenta and crystallize. Magwar then heads underground to speak with Envy. He assures her that dealing with the Elric brothers will not be a problem and that their cooperation is insured.
The next day, Magwar invites the Elric brothers to his mansion to do research on the red water. He entices them with a sample of crystallized red water. Ed agrees but asks to be allowed to punish the imposters first. In the underground jail, Ed frees the two brothers telling them to free themselves from the shadow of their past and move forward.
Revoking his pledge to help Magwar, Ed provokes the wrath of Magwar and his crystallized red water pieces. Cornered behind a pillar, the brothers are saved by Nash's sons. However, it appears that Magwar has escaped via an underground route.
The cannon fire from Magwar has affected the structural integrity of the underground caves, and the brothers are forced to escape. Unwilling to handover the spring of red water, Magwar is crushed by a falling slab of rock. In reality, the shock has destabilized the entire mountain side and has begun to collapse.
In order to save the town, Ed errects a giant stone barrier between the mountain and the town. Wanting to help out, Flecther makes the tress in rising pool of red water absort the water turning the trees red and causing them to vanish.
Leaving Xenotime by train, the brothers part with Russel, Fletcher, and Elisa.