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Cottle is known for his eccentricities (such as being a heavy smoker despite the obvious medical risks), outwardly abrasive demeanor, and being unimpressed by positions of authority. He is considered a "bastard" among some of Galactica's crew, but above all things he is a healer. To him, nothing else truly matters, be it rank, riches, or species. However, Cottle has shown a caring side that he hides under the gruffness. He comforts the mortally wounded Natalie as she dies by holding her hand and takes good care of Roslin. When Roslin brings this up, he shows he does care and is clearly affected by her words, but she has him return to his usual grumbling and smoking to save his reputation.
Cottle is the third person in the Fleet to learn about President Laura Roslin's fight with cancer, after Lee Adama and Billy Keikeya (TRS: "Act of Contrition", "Bastille Day", and Miniseries, respectively). He agrees to treat her condition, without revealing it to anyone else, and further agrees to support more unorthodox treatments, namely the use of chamalla extract (against his better judgment). Knowing the extent of her illness and Roslin's reluctance to undergo Doloxan therapy, the doctor also recommends prayer.
Cottle takes a personal interest in Kara Thrace's recovery from injuries suffered during a mission (TRS: "You Can't Go Home Again"). The doctor works with Lee Adama to get her out of sickbay (TRS: "Six Degrees of Separation") without initial success.
After the assassination attempt on William Adama, (TRS: "Kobol's Last Gleaming, Part II") Cottle is unavailable to stabilize the Commander as he is aboard another ship in the Fleet. Matters worsen after Galactica's jump to the emergency coordinates separates Cottle and the battlestar. Colonel Tigh orders Cottle's medics to stop Adama's internal bleeding (TRS: "Scattered"). However, while the medics stabilize the Commander's condition, they are unable to fully stop his bleeding. Cottle finally arrives and is able to operate on Commander Adama. After much risky work, the doctor saves Adama's life (TRS: "Fragged").
Cottle speaks rather contemptuously of Colonel Saul Tigh's authority. When Tigh asks of Adama's condition as Cottle begins surgery to save the Commander's life, he tells the XO, "How should I know? I'm not a psychic. Now get the hell out of here" (TRS: "Fragged"). Later, after Tigh orders an ill-advised attempt to restore supply runs to Galactica on the Gideon, resulting in four civilian deaths, Cottle is anything but sympathetic when Tigh asks what happened: "What'd you expect, genius? You put a pilot in charge of crowd control" (TRS: "Resistance").
At the request of President Roslin, despite her straight-to-the-point warning about its illegality and danger (Cottle: "You're a lousy salesman."), he assists Roslin in escaping Galactica by filing a request for a Raptor flight away from the battlestar, to care for patients on other ships. Roslin leaves Galactica on this "appropriated" Raptor with Lee Adama at the helm (TRS: "Resistance").
Major Cottle performs a series of medical scans on Gaius Baltar's head at Baltar's request. Unknown to Cottle, Baltar is looking to see if there is a Cylon computer chip implanted into his brain. The scans show absolutely nothing unusual, and Cottle dismisses Baltar as a hypochondriac ("There's one on every bloody ship.") (TRS: "Home, Part II").
Even Cottle's stony exterior gives way to the pain he sees on Laura Roslin's face when he gives her a new prognosis on her fight with cancer. Her cancer has spread aggressively, and the good doctor gives Roslin, on the outside, one month to live (TRS: "Flight of the Phoenix"). His concern for Cylon Sharon Valerii and her unborn hybrid child is remarkable, especially in the face of the rest of the crew's distrust and even hatred of her, hinting at his extremely strict sense of medical ethics. He describes her attempted rape by Lt. Thorne as "unforgivable," and voices his opposition to Baltar using Sharon's baby's blood as a cure for Roslin's cancer (TRS: "Resurrection Ship, Part I," "Epiphanies").
Cottle gains a reputation among the Fleet for performing abortions. When Rya Kibby, a young Gemenese girl, wanted to end her pregnancy, she stows away to get aboard Galactica and see Cottle. Cottle explains the situation to Admiral Adama by acknowledging, "I get a note that a girl's on the way. She arrives. I do my work. And then she leaves. I don't ask a lot of questions." When Admiral Adama asks Kibby to return to her parents, Cottle suggests that the girl instead request political asylum aboard Galactica, earning a stare from Adama (TRS: "The Captain's Hand").
After the election of President Baltar and the settlement of New Caprica, Cottle, like most of Galactica's crew, retires from military duty. One year after the election he serves as a doctor on New Caprica in private practice (TRS: "Lay Down Your Burdens, Part II").
During the Cylon occupation of the planet, Cottle continues his work as a doctor and surgeon. He works as a neutral party in the Cylon-run state in New Caprica City, treating human and Cylon alike. When a copy of Number Three (likely D'Anna Biers) questions why he does this he tells her he would do the same for anyone who came to him (TRS: "Exodus, Part I").
After the events on New Caprica, Cottle is forced to deal with varying cases of illnesses as Galactica takes on refugees. Among one of the diseases, Mellorak infection is discovered. Hoping to conserve as much of the dwindling supply of medicines as possible, he assigns the medication for Mellorak to Galactica personnel for immunization and all others on a need basis. Due to the inquisitive nature of Karl Agathon, the appointed "mayor of Dogsville," Cottle investigates the activity of his long time friend, Michael Robert. After performing extensive autopsies on a few of Robert's patients, Cottle discovers that Robert is killing patients based on their birth colony, mainly those from Sagittaron. Cottle, with help from Saul Tigh, puts an end to Robert's practices (TRS: "The Woman King").
Shortly after discovering that Laura Roslin's cancer had returned, Cottle starts Roslin's Doloxan treatment. After it is completed, he, along with his medical staff, are completely flabbergasted when Roslin and Sharon Agathon wake up screaming simultaneously. Unfortunately, it is not known whether he is informed of the vision that the two, plus Caprica-Six, shared (TRS: "Crossroads, Part II").
Cottle treats Gaeta when he returns from the Demetrius mission, but Gaeta's leg is so bad off with infection, Cottle doesn't even try to save it, immediatly calling for a cut-down tray for amputation. Cottle tries to disuade Gaeta from remaning awake during the operation, but is sympathetic and agrees when Gaeta explains why. Cottle amputates Gaeta's right leg beneath the knee (TRS: "Guess What's Coming to Dinner?")
Cottle treats the mortally wounded Natalie and tries to save her life, but fails. As she dies, she reachs out to him and he takes and holds her hand as she dies, offering her some comfort as she dies with no hope of resurrection (TRS: "Sine Qua Non").
When Adama plans one final mission for Galactica, Cottle and Ishay discuss it in sickbay, not realizing Laura Roslin is listening. When Adama calls for volunteers for the rescue mission, Cottle and Ishay both volunteer, but Adama sends Cottle back, calling him by his first name and telling him that he's too valuable for the Fleet to lose (TRS: "Daybreak, Part I").
Later he gives Roslin injections to keep her on her feet for two days so she can perform in the rescue, but he warns her doing so will use up what little life she has left. Roslin thanks him sincerely and Cottle is truly touched and seems to be almost about to break down, which Roslin notices and tells him not to ruin his image and go and smoke a cigarette with a gruff attitude. He's later seen on New Earth as part of the landing party that investigates the tribal humans they find. He explains he examined a grave and the DNA of the humans on the new Earth is compatible to the Colonials (TRS: "Daybreak, Part II").