Previously in part one...

The Athena, assigned to travel to the remote dilithium mines at Delta Vega, intercepted a Jem'Hadar ship attacking a civilian starship deep in Federation space. After destroying the attackers, the crew of the Athena rescued two survivors, including a Changeling named Unid. The individual, who had lived on El Nanth, came on board with a plan to convince the Dominion forces to retreat from Betazed without the invasion many feared would be necessary. After some discussion, Captain Thorpe agreed to the plan and took the Athena to Betazed. At the planet, after slipping through the Federation blockade, Thorpe and some of his officers, along with Unid, met with the Founder in charge of Betazed, only to find him suffering an advanced case of the Changeling disease that was affecting the shape-shifters throughout the quadrant. Because of his state and the state of Dominion forces overall, the Founder on Betazed, with barely any negotiations, agreed to leave the planet peacefully and return to the Gamma Quadrant. Thorpe then exposed his ship and informed the blockade leader about what he had done and what he needed to do now. The blockade leader was skeptical, which Thorpe did not find surprising. Afterall, he already knew that an element in Starfleet Command, fronted by Captain Nathan Totten, did not want any information about the Changeling disease to get out, or for Betazed to be liberated so easily.

And now the conclusion...

Captain Thorpe beamed down to the Betazoid capital again, to the same area where they had beamed down earlier. He was accompanied just by Doctor Psakolaps, who was carrying a medical kit, and Lieutenant Hakamura, who was the only one armed with a phaser rifle. Unid was also with them, since he was always the insurance that the Jem'Hadar would not simply fire on them. However, when they rematerialized, the Jem'Hadar were waiting for them, weapons down, along with a Vorta. It was the bureaucrat who stepped forward, saying, "Do come with me."
      The group marched through the huge anteroom leading to the royal chambers, but this time, there was no waiting, just a simple trek across the marble floor to the other side. The doors were opened for them, and at the end of the second corridor, the other doors were also open and waiting for them. The room looked different now. The Dominion equipment was all gone, and apparently the Betazoid artwork-gaudy was too gentle a term for it, Thorpe felt-was restored to the wall. The Founder, however, continued to sit behind the desk, his appearance seemingly wasting away with each fleck of dried-up protoplasm that peeled off of his body.
      Speaking in weakening tones, the Founder said, "We have upheld our end of the bargain. Our forces, except for the tiny contingent guarding me here, have returned to the ships. We have left the planet untouched, and once again, the Betazoids are taking charge of their own affairs. I do not believe they could rule this planet as competently as we do."
      "A view I'm sure the Betazoids don't share," Thorpe pointed out.
      "So again, we'll let the Federation rule them. Afterall, what is the difference really?"
      "Betazed voluntarily joined the Federation."
      "Other worlds have joined the Dominion willingly," the Founder remarked. Thorpe quickly wondered why a planet would, but then the Founder gave the example. "Cardassia is one." Then the captain wondered why a world that was not demoralized or militarily weak or which lacked confidence would willingly join the Dominion. Then he recalled the Breen.
      "That may be true, but the simple fact is, if Betazed wanted to become independent and leave the Federation for whatever reason, they could do so without Starfleet surrounding the planet and threatening it. Could the same be said for the Dominion?"
      The Founder wanted to say something, but then changed his mind. His condition was worsening, and Thorpe had to feel a bit of empathy for the being. Afterall, he could see this particular Founder as an individual, and not as a part of a collective mass of unrelenting evil. As an individual, there was always the chance that he could see the error of his ways, and attempt to rectify the problem, and maybe there was some of that here. Being on Betazed for over a year might have been enough to suggest to him that the fear of the Federation was overrated, or at least the more basic kind of fear that the Dominion operated on was overrated.
      Struggling to stand up, the Founder said, "We believe it is time to depart. I trust you were able to convince the ships in the blockade to let us pass."
      "I'm working on that. I doubt that they will attack as your ships move out."
      "I have my doubts about that."
      "I'm sure you do," Thorpe remarked.
      Doctor Psakolaps stepped forward, and said, "Founder, I do have one request to make." The shapeshifter stopped and turned to look, up slightly, at the Kentyan medical officer. "I want to take a sample of your protoplasm."
      "For whatever reason?"
      "With Unid, I have a Changeling who is unaffected by this disease. By comparing a sample of his protoplasm with yours, I hope that I can attempt to isolate the disease. If it was in fact a biological weapon, I want to know how it was done and who was behind it."
      "It was not you?"
      "No," Thorpe admitted. "This is something that was not done by Starfleet and which would not be condoned by the Federation. Defending the Alpha Quadrant and maintaining our freedom does not require the genocide of an entire race, and I believe that it was wrong. Who is behind this surely is not following the beliefs and philosophy of the Federation. It is important to find out what is going on here."
      "You would do that... for your enemy?"
      "We have to think of the period after the war."
      "I guess we do. Very well." The Founder recognized the protoplasm sample gathering device that Psakolaps removed from the medikit, and he held out his arm as the doctor placed the tip against his flesh. Within several seconds, Psakolaps had withdrawn about five cubic centimetres of the fluidic protoplasm of the Changeling. He looked at it. Instead of the sparkling gold colour he was expecting, he found the sample streaked with a pale bluish-green.
      "We must get back to the ship."