DS Andrew Flanagan was the detective who, alongside DS Shields, oversaw the investigation into Alex Moss's murder in 2013. He also investigated Ross Barton's acid attack in 2018.
Following Katie Addyman's anonymous tip off that there was a body buried at Home Fields Glamping Site, DC Flanagan and his colleague DS Shields appeared at Home Farm to speak to Declan Macey. A few days later, workman Thomas Hillam informed the police that had Declan paid him to cover up a suspicious object that was found whilst digging the foundations of the glamping site. Hillam showed the police were to dig and subsequently they uncovered human remains. Declan was arrested for perverting the course of justice and Shields and Flanagan interrogated him about the body as well as Katie's sudden disappearance. The body was later identified as Alex Moss.
After punching Declan, Adam Barton was arrested for assault. Whilst being questioned over the assault, Flanagan and Shields took over the interview and interrogated Adam about Alex's murder, suggesting that Alex's relationship with Adam's mother Moira could be his motive. The police later found a glove covered in Adam's DNA that Cameron Murray had planted near to where Alex's body was buried. Adam soon discovered one of his work gloves was missing and realised he was being set up. Whilst the police searched Butlers Farm, Moira's boyfriend Cain Dingle distracted the police officers which allowed Adam to escape and go on the run.
A few days later, Chas and Debbie Dingle went to the police as they suspected Cameron was responsible for Chas' sister Gennie Walker's death and believed he may also be responsible for Alex's murder. Flanagan and Shields questioned the women, but as they didn't have enough evidence to arrest Cameron, they suggested putting hidden cameras in Debbie's house to get a confession. Although reluctant, Debbie agreed. After Cameron referenced killing Carl King out of reach of the cameras, Debbie insisted on wearing a wire to catch his confession again. Flanagan and Shields were against the idea but went ahead with it. Debbie was able to get a now suspicious Cameron to confess but told him about the wire and cameras and as a result Cameron locked all the doors and held Debbie hostage. Debbie managed to escape and Cameron was arrested.
The following month, Flanagan informed Debbie and Chas that Cameron had escaped from a prison van. After laying a false trail, Cameron headed back to Emmerdale and took a group of villagers hostage in The Woolpack including Debbie and Chas. Debbie and Chas managed to escape Cameron's clutches and Cameron was electrocuted to death.
Six months later, Debbie contacted Flanagan after learning about the Domestic Violence Disclosure Scheme, known as Clare's Law, and asked him to do a background check on her new boyfriend Pete Barton to make sure he wasn't like Cameron. Flanagan learned Pete had an old conviction for assault years prior which made Debbie reassess her relationship.
In September 2014, Flanagan questioned Declan's sister Megan about positioning Declan's step-son Noah. Megan protested her innocence and theorized that Declan's wife Charity was trying to poison Declan. Megan worked out it was actually Declan poisoning Charity and tried to leave the interview room but Flanagan stood in her way. During an altercation, Megan slapped the detective earning her an extra night in the cells.
In early 2018, Flanagan was involved in the investigation into Ross Barton's acid attack. Whilst returning Ross' laptop, Flanagan told Ross off the record that police were closing in on a suspect. After Simon McManus was arrested, Flanagan showed Ross mugshots hoping he would be to identify his attacker but Ross could not. Ross suggested Debbie have a look at the photos to see if the man she argued with prior to the acid attack was there. Debbie spotted the attacker, but lied she didn't recognise anyone to hide her own involvement in the attack. Although Ross couldn't identify his attacker, the police were able to charge Simon with the attack as a witness had come forward to say he heard Simon mouthing off about the attack and they also have CCTV footage of Simon purchasing the corrosive substance. Simon was found 'Not Guilty' of the acid due to the death of the key witness which meant the key witness' evidence was inadmissible. Subsequently, the case was closed.
Whilst being interviewed on an unrelated charge in June 2018, Debbie's thirteen-year-old daughter Sarah revealed Debbie paid Simon to carry out the acid attack. Flanagan, who had been promoted to DS, and PC Swirling called round to Jacobs Fold to speak to Debbie, but before they could, Sarah collapsed and was rushed to hospital. The following day, Flanagan and Swirling spoke with Debbie. She denied the allegations and claimed Sarah only said it to get back at her. Although unconvinced, Flanagan had no evidence to the contrary.