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In the build-up to the wedding Flynn turned a hero when Sophie went into labour at the bottom of a cliff. Flynn was out camping with his mates nearby and he then abseiled down the cliff to deliver the child.
Come the wedding day, everything went wrong. Scott's horse, Jacko, bolted, leaving Leah and Sally stuck out in the countryside. As Leah and Sally made their way to the wedding, Flynn was left wondering whether he had been ditched at the altar. Leah and Sally, soon turned up, a little worse for wear.
Just as the wedding was about to get started it was hit by a sudden thunderstorm and they had to run for cover. Eventually the bedraggled couple and guests made their way to the hospital where Donald married Sally and Flynn in the reception, alongside Sophie and her newborn. They then went off on their honeymoon bought by John.
When they returned Flynn found that his surgery had been finished. Colleen quickly offered her services as his assistant and despite having her lack of computing skills, Flynn took her on. Unfortunately Colleen was one of Flynn's first patients as he diagnosed her with breast cancer. Sally and Flynn were there as a pillar of support through Colleen's ordeal from which she eventually recovered.
Another of Flynn's early medical stories was the discovery of a mysterious child on the rocks. He tried for days to work out what language she was speaking and where she had came from. With Sally's help they discovered that she was speaking Pig Latin and her name was Tasha Andrews. Flynn legally adopted Tasha, though Irene looked after her.
Flynn soon found himself held hostage by Kane's brother, Scott Phillips in his surgery. However Flynn in a moment either of supreme bravery, or real stupidity, tackled Scott and won. Scott managed to escape.
Flynn also tried helping Seb through a difficult period during his life when he found himself dumped by Kirsty. In an attempt to win Kirsty back around Seb began starving himself and Flynn tried talking Seb around.
Sally revealed that she had one last egg left with which to attempt to have a child and this time friend, Leah Patterson offered to carry their child. After discussions between Sally, Flynn, Leah and Jesse they decided to go ahead with it and have the treatment. It was a success and Leah became pregnant.
Their joy almost didn't last long after Leah told her parents about what she was doing. On the way home they crashed their car. However both Leah and the child survive.
Flynn continued investigating Tasha's past and after one trip he delivered the news to Irene, her mother was Angela Russell.
Sally's old friend, old in more than one way, Floss returned to the bay and told Sally and Flynn that she was dying for cancer and asked Sally to help her end her life. Sally eventually decided that she would help Floss go through with it and sneaked into Flynn's office and took some morphine out. Flynn soon discovered the missing medication and had a showdown with Sally, about her deception. It was revealed that Flynn helped his mother end her life and how he now lives to regret it. Flynn soon discovered that Floss had been mistakingly misdiagnosed and didn't actually have cancer.
Flynn also discovered that Kirsty had been lying about being pregnant with Kane and at the same time discovered that she was pregnant with Kane. When he mistakingly let the information slip to Kane about Kirsty's deception Kirsty and Kane briefly came to blows.
Flynn began spending more time with Leah as the birth of his and Sally's baby approached and they soon ended up sharing a kiss, but they were caught by Jesse. Sally soon found out about this and left the bay, leaving Flynn fearing for his marraige. Sally soon returned and they managed to continue their relationship. Leah and Jesse weren't quite as lucky. However it was during a heart to heart with Jesse that Leah went into labour and Jesse got her to hospital. Flynn and Sally were out celebrating Flynn's birthday at the time and the members of the bay struggled to get in contact with Flynn and Sally. They did soon and Sally and Flynn raced to the hospital where Leah gave birth to baby Pippa, despite Colleen being under the impression that it was going to be named after her.
Flynn soon got caught up in all that was happening with Sarah Lewis wreaking havoc around the bay and for the second time in less than a year he ended being held at gun point and after trying to overpower Sarah, Noah Lawson was shot.
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