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Following his dismissal from the school, Don started working at the drop-in centre. However Flynn soon fell out with him (noticing a recurring theme here), citing Don's career as headmaster creating the wrong impression for kids visiting the centre. Don however proved Flynn wrong when he solved a bullying case.
Flynn then came to Noah's rescue after Noah collapsed in the drop-in centre, suffering from meningitis. This caused the drop-in centre to close briefly, but it soon reopened and Flynn had a new case to deal with, Dani's rape mediation with Kane Phillips. Much against Shelley and Rhys' wishes, the meetings went ahead.
The first meeting was a disaster with Kane and Dani ignoring all rules set out, but Dani wished to have another go and a week later the meeting was more succesful and some closure was found. Flynn showed his caring side soon after. On the date of his 30th birthday he managed to organise for all of Sally's old brothers and sisters to go back to Summer Bay House to watch a tape sent from Pippa.
Flynn and Sally then went aboard the Mirigini as part of the celebrations. Once the boat was sunk in a storm, Sally and Flynn ended up apart. Whilst Flynn was found within a couple of hours, Sally was still lost in the bush. However, thanks to the skills that Flynn had taught her about surviving in the bush, she helped both Blake and Sophie survive.
After organising a session for the survivors of the boat disaster Flynn soon discovered that Kirsty and Kane were involved in a relationship. However following Kirsty's wishes, Flynn didn't tell anyone, though he continually advised Kirsty that the relationship was bad news. Soon Shelley found out about the relationship and discovered that Flynn already knew, straining their working relationship.
The drop-in centre was soon robbed and the computers stolen. During the clean up operation it was discovered that Flynn had forgotten to renew the insurance. It was later discovered that Kelli's husband Jason had stole them. In a bid to pay for the insurance Flynn agreed to do some modelling - nude modelling. This later caused problems for Flynn when Josh's mother, Jackie wrote a story about whether or not Flynn should be working with children. However Shelley and Josh helped talk Jackie around and the story didn't run.
Back to the photo-shoot and Flynn encountered a pregnant photographers assistant named Mia. Flynn gave her his number and a couple of weeks later Charlotte found a baby left abandoned at the drop-in centre. After her recently losing her baby, she wanted to keep it. Flynn got in contact with Mia and mother and child were soon reunited. Eager to have a child, Charlotte asked Flynn if he would help her. This caused problems between Sally and Charlotte. Charlotte soon died just before leaving for Vietnam and Flynn helped Jude through his speech. Charlotte bequeathed Flynn her medical books.
Sally and Flynn decided in late 2002 that they were going to look into alternative methods of having children. Sally told Flynn that she had saved some eggs from when she had had her cancer discovered the year before, and they began to look into surrogacy. Sally bumped into an old school friend named Tara and for a while it looked as though she would be the one to provide Sally and Flynn with a child. However Flynn did some investigating into Tara's past and found out that Tara had ran away from home after being responsible for the death of her husband and youngest child and they decided Tara was not suitable. Angela Russell offered, but again they decided to hold off. Sally then got one of her former foster sisters, Sophie to come across the country.
Sophie was initially peeved off when she discovered Sally's underhand reason for getting her to visit, but she was eventually talked around by Irene and three of them headed off to get the tests done and the procedure started.
When Flynn and Sally returned , Flynn had undergone a drastic makeover (due to an actor swap) and they began to look forward to having their child. Sophie was brought across to live with them. At was at this time though that Flynn began questioning whether he still wanted to be a counsellor and he began looking into opening a medical practice.
Flynn also tried helping Angie as her behaviour became more and more estranged. However tragedy soon struck as Sophie collapsed at the beach house and miscarried Sally and Flynn's child.
A few wakes later, after continously trying to find the right moment to propose and even having moments of self doubt over whether it was the right decision, Flynn proposed to Sally at the school and she accepted.
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