Andy and Jo married on 19 February 2008 in prison. Jack, Victoria, Daz, Ashley and Laurel were their guests and Ashley presided over the service. Jo did not want to marry in prison but wanted to please Andy. She also persuaded Bob Hope to let Debbie borrow the keys to Tug Ghyll so she could get her post – particularly adoption papers for Sarah. One day, when Jo went to visit Andy, she asked Debbie to watch Sarah. Unfortunately spending time with her daughter meant they started bonding so the adoption was cancelled.
Andy returned from prison to find that everything had changed. Ex-inmate Charlie Sellers had stored guns in the barn, the farm was losing money and Jo had lost the lease, due to Charlie taking the rent money. Diane took over the lease and was happy for Andy to run the farm but he was angry - he felt Diane wasn't part of the family as she and Jack had separated. He also discovered that Jo and Debbie were friends. Debbie, Chas and the McFarlanes forced Charlie to leave the village after he threatened Sarah but he insisted that Debbie had made matters worse. Then he discovered Debbie had not signed the adoption papers. He visited his solicitor, hoping it would be approved regardless but was told that would only happen if Debbie was a danger to Sarah.
All of this had a negative effect on Andy, as well as the fact that being in jail had been difficult and had changed him. When he realised Jo had allowed Debbie access, he lost his temper and lashed out giving Jo a black eye and Andy promised her it would never happen again.
In June, they celebrated Sarah's 3rd birthday and Jo could see Andy was getting agitated, particularly when Sarah loved the doll's house that Debbie had bought her. Andy had made Jo return the doll's house, insisting it was too expensive so Jo told Debbie that was what Sarah wanted. Wanting Sarah out of the way, Jo took her for a bath and Andy destroyed the house.
Over the next few months, the abuse continued but Andy and Jo made up. They disagreed repeatedly, particularly about having a baby as Sarah mentioned having a sister. Andy wanted a baby but Jo did not, and when Sarah saw Andy grab Jo's arm, Jo asked him to leave. Feeling sorry for himself, Andy got himself drunk and went missing. Daz brought him back home but he had made himself so ill, he had to be confined to bed but later recovered.
Andy and Jo's last argument was over Jo's "pregnancy". Fearing another beating, she told him she was pregnant. Andy was thrilled but Katie was suspicious when she saw Jo with Debbie and told Andy. He gave Jo a pregnancy test, wanting proof so Jo admitted she'd lied. She tried to leave but Andy wouldn't let her go, leading to a fight in the barn. Andy was admitted to hospital, seriously injured. Jo told the Sugdens about Andy's abuse but Daz and Victoria didn't believe her until they saw Andy attack her. Alone in the farmhouse, Andy threatened to kill himself but Diane stopped him. She took him to hospital and arranged for him to have psychiatric treatment.
Jo agreed not to call the police if he moved out so he moved in with Diane and Katie gave him work. The reasons for Andy and Jo's split were soon public knowledge. Katie also gave Andy a shoulder to cry on and supervised his time with Sarah. Shortly before Christmas, Sarah was suspended from nursery for fighting and missed the Christmas play that she was eagerly looking forward to. As a result of this Diane, Andy and Katie staged a play in the Woolpack. Everything went well until Daz saw Andy and Katie kissing. Andy thought Katie wanted him back and lost his temper when she said she was happy single. Horrified by Andy's attitude, she sacked him. When she learned Jo knew that Andy had kissed her, she visited Jo and convinced her that she and Andy were history. Katie suggested Jo leave if she wanted Andy out of her life. Jo wasn't sure but Katie said Andy would always be there while she had Sarah and Jo realised Katie was right. Andy tried winning Jo round by vandalising farm equipment, knowing he was the only one who could fix it. Daz and Lee Naylor were suspicious but couldn't prove it until Lee caught Andy vandalising the washing machine. This made Jo decide that she had to get away. Lee helped her sell the farm equipment and she left just after Christmas, after leaving Sarah with the Dingles. Andy was shocked that Jo had left and was worried that she'd taken Sarah but found her at the Dingles so he returned to his farm.
Life on the farm without stock or equipment wasn't easy but Andy managed and lived quietly for a brief period, visiting Sarah frequently but wasn't allowed to take her home. Debbie, Sarah's mother, insisted she stay with the Dingles. In February, he and the Sugdens heard that Jack had died. Diane went to Spain to collect his body and he was buried in the village churchyard. Annie came too and gave Diane a letter to read at the funeral, in which he asked Andy to take over as head of the family. Andy initially refused but agreed after he saw Robert, his adoptive brother, watching from a distance. When Robert saw Andy, he left but before he did, he told Andy that there was nothing for him in Emmerdale.
As head of the family, Andy decided he wanted his daughter back, as her mother was now in prison, awaiting trial for murder. Diane asked the Dingles to let her take Sarah, threatening to go to a solicitor if they refused. Zak and Lisa agreed but made Diane promise she would return her immediately, if she felt there was any danger. Diane agreed and Sarah returned to Butler's Farm, living with her dad, uncle Daz and auntie Victoria. When Debbie was released from prison, she asked for more access to Sarah. Andy wasn't happy about it but Diane convinced him it was a good idea. Debbie tried to discuss access with Andy but he was awkward so she warned him she wouldn't give her daughter up without a fight.
Maisie Wylde made it clear she fancied Andy as soon as she saw him. Her family were concerned and told them to end things so they kept their relationship secret. Debbie found out when she found Sarah apparently alone in the farmhouse. Andy and Maisie weren't far away but Debbie was angry with Andy for neglecting Sarah and said so. Andy asked them both to leave, so Maisie warned her not to try to cause trouble between her and Andy. Diane stopped them fighting and told Andy to end things with Maisie. Andy ignored her and Maisie moved into Butler's Farm. She was happy to stay initially but moved out when it became clear that Andy expected her to help out with the farm and with looking after Sarah. Andy continued to be difficult about Debbie seeing Sarah. One day, Sarah saw Debbie in the village and asked if she could play at her house and Andy agreed but later changed his mind. Debbie warned Andy that he couldn't change his mind just because he felt like it. He ignored her until he got a letter from Debbie's solicitor, telling him she wanted custody. Andy discovered that Debbie's father, Cain, was back when he and Debbie visited, bringing Sarah a fairy's outfit. Later, in the pub, he told her and Cain that when he won, they would never see Sarah again. Debbie tried to reason with him the next day but he wouldn't listen.
On the day of the hearing, Cain saw Andy and Sarah with Val and taunted Andy that soon he and Debbie would be putting Sarah to bed at night. Andy said that wouldn't happen and left. Cain followed, telling Andy that CAFCASS take domestic violence very seriously. Realising they knew about him abusing Jo, Andy tried to knock Cain down but Cain jumped out of the way and called the police. They questioned Andy about dangerous driving when he was meant to be in court so the hearing was postponed. Debbie was angry with Cain but when Andy visited later, she told him she was pleased Cain had reported him as she felt he was out of control. She threatened not to let him see Sarah if she won. At the hearing, Andy withdrew his application and by default, Debbie won. Losing custody of his daughter was a massive blow to Andy.
By June 2009, after everything he had been through in his life and the recent loss of Jack, Daz (whom he ordered to leave the village after the shock of discovering that he and Victoria were having a sexual relationship) and now Sarah, Andy began to have a breakdown. Friends were noticing that he seemed vacant, Sarah called out to him in the street but he didn't acknowledge her, and Victoria spent a night with Diane at the Woolpack and came back to find that Andy had packed her bags. Hurt, she moved in with Diane. Mick Naylor, the farmhand, couldn't understand what was wrong with Andy. Thinking he was just being lazy (Andy sat about watching TV and drinking tea, instead of working), Mick quit, and soon left the village along with grandson, Lee (who had a relationship with Katie Sugden, causing more stress for Andy who still had feelings for Katie and would admit the following year, that the only reason he got with Jo was to get back at Katie's affair with Robert, but Katie was remaining just friends with Andy). Paddy Kirk, the local vet, suspected something was seriously wrong when he visited and found the farmhouse in a state. He was concerned about the cattle's inoculations but Andy refused to discuss it. Katie also asked if she could move her stable business back and initially Andy agreed but when she turned up with the first horses, he sent her away again. Katie was concerned when she realised Andy thought they were still married. Eventually, she and Diane persuaded Andy to move to the village when it was clear that the farm had to be closed down as some of the animals were ill. The doctor visited Andy at the Woolpack and diagnosed clinical depression. He was referred to a specialist and put on a course of medication.
Andy repaired and strengthened his friendships with the other Emmerdale residents, including Katie, during and after his recovery and settled back into normal life, living in the village and travelling to Butlers Farm to work for his successors to the lease, The Barton family. At Butlers, Andy made new friends with John and Adam Barton, whom he worked alongside, and enjoyed doing farm work again. Happiness also returned to Andy's love life when factory worker Adele Allfrey showed an interest in him, but Andy was hoping for a reconciliation with Katie (who had a brief romance with Ryan Lamb during this period) and was reluctant to respond. However, after almost accidentally running her over in the street, Adele asked him to buy her a drink and they dated for a while. They separated after Andy returned to his old ways of showing displays of jealousy, temper, and controlling behaviour while with her. Adele was not prepared to put up with this and left Andy and moved out of the village.
Andy then sought professional help to resolve his remaining, underlying emotional issues. However, the therapy seemed to make things worse. When he returned from a session and Katie supportively asked how things had gone, he blamed her for all his troubles in life as the therapist had asked him to talk about his first girlfriends. He said he realised that it all stemmed from her cheating on him with Robert when they were first together when they were younger. Katie was his first love, made him feel happy after the family problems he had been through as a child including losing his adoptive mother, Sarah, and Robert blaming him for it. Andy then revealed that when Katie began an affair with Robert, that was the start of things continuing to go wrong for him. Katie was shocked that Andy was blaming everything on her because of the mistake she had made when she was very young, but she comforted him and the two ultimately ended up sharing a night of passion. The next day, however, Katie told Andy it had been a mistake and they should only remain friends and to seek romantic happiness separately. Andy reluctantly agreed.
In November 2010, Andy becomes jealous when Katie starts a relationship with police officer Nick Henshall.
In January 2011, Andy is accused of starting the fire that killed residents Viv Hope and Terry Woods. It is later revealed police officer Nick Henshall started the fire to try and frame Andy. Henshall is then arrested after kidnapping Katie and holding her hostage when the truth comes out.
Andy begins a relationship with Alicia Gallagher in February, 2011 they break up a couple of times but get back together but eventually break up fully in January, 2012 after Andy decides that daughter Sarah is his main priority.
In late 2011, Andy and Debbie's daughter Sarah becomes ill and she is then diagnosed with Fanconi Anaemia, a genetic disorder which could kill her without treatment. Debbie and Andy then go about looking for donors to try to save Sarah but having no luck in finding a donor, they believe having another baby also known as a 'Saviour Sibling' is the only way to save their sick child. They apply for IVF but get turned down when the hospital find out they are pretending to be a couple in hope of getting accepted to have the IVF. This is a big shock for the pair and they do not give up. Debbie suggests having a baby by using artificial insemination, with their partners Cameron and Alicia still not happy with the situation of them having another baby together they choose to go along with the process anyway but have no luck after trying numerous times. Debbie believes the only way to conceive is for them to sleep together. Andy is unsure at first but eventually agrees to the plan, their other halves are upset and angry that they have to do this, resulting in Alicia breaking up with Andy but Cameron still agreeing to support Debbie through this whole situation. They plan to sleep together but Debbie can't through with the plan and walks out on Andy leaving him humiliated, she then tells Cameron they never went through with it and he tells her if she had he would have walked out on her. Desperate to save her daughter, Debbie gets Andy to meet her at a hotel, she says she's sorry for her previous actions and eventually gets him to sleep with her after seducing him and telling him it is just about them and that she wants him. After sleeping together, Debbie doesn't tell Cameron they have and Andy is confused with his feelings for the mechanic. He becomes jealous of Cameron and turns up Tug Ghyll at any given chance just to see Debbie. Debbie discovers she's pregnant and Andy is delighted, while Cameron feels left out but still believes the baby was a result of artificial insemination. Cameron becomes angry that Andy is always there and won't leave Debbie alone, he then warns Andy to stay away.
On February 16, 2012 John Barton dies in a car accident after skidding on ice while using Andy's land rover, Andy is guilt ridden after he finds out and thinks his car was the cause of the accident, Moira assures him it was icy and that he is not to blame. Andy breaks down and tells Moira he feels like he has lost a brother after he and Moira talk about his and the Barton's first meeting on the farm. He feels depressed and Debbie tries her best to console him without getting to close, he then reveals he loves her, this shocks Debbie and she tells him she doesn't love him, Cameron's the one she loves. Andy is heartbroken after Debbie is quick to leave. After having an argument with a snappy Debbie, Cameron knows something is up and heads straight to Andy's, demanding he stay away or else. In his rage, Andy admits he and Debbie did not conceive the baby using artificial insemination, they slept together. This leaves Cameron angry and hurt, Debbie lied to him.
In March 2012, Andy and Debbie find out their baby is match for ill daughter Sarah after Debbie undergoes test. Cameron and Debbie eventually get back together after Debbie admits he is the only person she has ever truly loved, Andy is hurt as he loves Debbie but she does not feel the same about him, Andy's jealousy towards Cameron continues.
In April 2012, Debbie finds out her and Andy's unborn child is a boy. The Dingles and Sugdens are delighted by the news but Cameron begins to feel left out even after Debbie's best efforts to get him involved with her pregnancy. Andy also gives his ex Katie advice after she breaks up with boyfriend Declan Macey.
In September 2012, Andy takes in Kerry Wyatt after her daughter Amy chucks her out, He confides in Kerry about his past and they both bond of what they both have been through. She cooks dinner for Andy and he tells her to stay another night as they kiss.
On 17 October 2012 during Emmerdale's anniversary live episode, Andy along with the Dingles is beside Debbie when she gives birth and is delighted when their baby boy is delivered. They name him Jack, after Andy's adoptive father.