Author's note: The idea of a Farscape crossover that has Crichton commanding a Colonial Battlestar was inspired by the story "Battlestar Farscape" by Mackon. However, that is where similarities end. This chapter may seem a bit rushed, but I want to end the flashback and move on with the main story line. There will be more flashbacks in later chapters to show what happened before the Pacifica found Starbuck.
Two days after finding the civilian ships, Crichton's fleet, which now consisted of Pacifica, Moya, and the bulky yellowish freighters with the civilians, had arrived in orbit around Carillon. The crew of the Pacifica had successfully managed to evacuate the survivors from the non-FTL capable ships onto the mysterious fleet of freighters they had discovered and jumped to the rendezvous coordinates mere moments before a large wave of Cylon raiders arrived. They now had food, water and medical supplies to last them for a long time, as well as plenty of living space. However, they needed to restock their Tylium supplies and for that reason Crichton had set course for Carillon, a supposedly abandoned mining outpost on a planetoid that barely supported life, according to Lieutenant Hill. Carillon was located in a neighboring star system and rich in Tylium and other raw materials.
Before they had jumped out, Crichton had his people rig the now abandoned civilian ships to overload their reactors as soon as they were approached by attacking Cylons. Using the abandoned ships as bait for the Cylon raiders, Crichton managed to buy his fleet enough time to jump out.
On the way to Carillon the fleet had made a stop at the rendezvous coordinates where Crichton's family joined the fleet aboard the Leviathan Moya. The Colonials had bought his cover story about Moya being an alien ship that had been discovered and studied in secret by the Colonial Government, at least for now. Aeryn told him how she had to fend off a Cylon boarding party and how Pilot finally had managed to flush them out by routing Moya's super coolant through the lower tiers.
John Crichton still had a lot of reading to do, if he didn't want to be caught. Impersonating a military officer is a serious crime in any society and if he got caught he would probably be thrown out of an airlock. He looked at the stack of books and decided which one to pick first. He had found books about the history of the Twelve Colonies, Military protocol, tactical capabilities of ships and fighters, and a few others. Luckily, he was good at improvising and he had impersonated a Peacekeeper officer on at least two occasions in the past. So far things had worked out for him and nobody seemed to be suspicious. The crew had even voted to promote him to Commander and made him the official CO of the Pacifica.
During his promotion ceremony, which was conducted by his command staff and a priest, Crichton got a taste of the Colonials religion. He had already known from the files the mysterious Doctor had given him that the Colonials worshipped the gods of ancient Greek mythology. He had a hard time remaining serious and not making any comments that could offend the Colonials.
The Pacifica now had a full command crew again, after Crichton had filled empty positions with former pilots who had been grounded due to injuries that prevented them from flying but not from performing shipboard duties. At the moment the Pacifica could only field three full viper squadrons and they had more pilots than vipers anyway. Crichton's goal was to mine enough resources at Carillon to produce at least another full squadron of vipers and another five raptors to replace at least some of the losses from the battle for the Colonies. He was planning to eventually have a full fighter and raptor complement again, plus some extra to station aboard Moya. New pilots would be trained from volunteers recruited from the civilian population. Sheba Cain was promoted to Captain and her assignment as CAG was made permanent. She had proven herself as a resourceful and competent leader protecting the civilian ships with Pacifica's viper squadrons.
While trying to figure out some of the more sophisticated controls, one of the civilian pilots, who now flew the ship that had transmitted the strange (to the Colonials) song, had found a mysterious file on the onboard computer. Every time he tried to open the file, it asked for the name of his parents as password. He typed in the names of his own parents a few times, but without success. Eventually he decided to contact the Pacifica and reported his findings to Commander Crichton. Remembering the song, Crichton knew that the file could have only been meant for him, so after making sure he was alone he entered the names of his parents.
A middle aged man with black hair and a goatee appeared on the screen. He was dressed in a black suit and began to speak, addressing Crichton by name: "John Crichton, I am Chief Zed, director of a secret organization that is protecting Earth. One of my associates, whom you may know as the Doctor, has informed me that you are leading a fleet of human refugees and together we have decided to send you these ships loaded with supplies. It is important for the safety of humanity that you do not lead these refugees to Earth. It is my understanding that the refugees are being followed by the machines who destroyed their civilization, and that these machines would do the same to ours. While we can defend ourselves better than you may think, we are not ready to repel a full scale invasion".
After watching the recording, Crichton ate a peanut butter and jelly sandwich from the food supplies from one of the freighters. He had forgotten how good it tasted, after not having had any food from home in several years. In the past week alone, things had changed so much for him. He was now in command of an entire fleet full of refugees, fleeing from genocidal robots who wanted to exterminate all humans. He could not go back to Earth, and then, an hour ago he had learned that Aeryn was pregnant with their second child. She told him she had the strong feeling this baby was going to be a girl and wanted to name her Xhalax, after her mother.
The destruction of the colonies just less than a week earlier had abruptly changed the lives of all the survivors in Crichton's fleet. John Crichton was at least used to being on the run. One of the people who were slowly coming to terms with the changes in her life was Major Sandra Robbins. A few days ago she had realized that she actually was a Cylon. She could have, should have destroyed the Pacifica back then, according to her Cylon programming. But something was stronger. And that was the loyalty to her crew. She realized that they were all individuals, who had families, had hopes and dreams. At least before the fall of the Colonies. They had treated her with respect; some of them had even become her friends. And then she was supposed to kill them all. But she couldn't. And she wouldn't. She would do her duty as an officer in the Colonial Fleet and protect what was left of humanity.
There were many things that struck her as odd about Commander Crichton. She had the feeling that he was not who he appeared to be. His whole mannerisms and his unorthodox command style seemed so strange to her. But on the other hand, Crichton was not a Cylon. She knew that, because she had seen all of them. Even those mysterious 'Final Five' and the no longer existing model Seven. When she had been unconscious, she had accessed parts of her memory that had been suppressed. She now knew secrets that not even most of the other Cylons knew. She had to tell someone, but that would mean admitting that she was a Cylon herself. Crichton was her superior officer now, but could she trust him? He has clearly shown that he was a capable leader and concerned about the wellbeing of the fleet. For that reason Sandra had suggested to officially promote him to Commander. But she could sense that he seemed to have his own agenda. She decided to wait and observe him.
End flashback