John Bates is Robert Crawley's valet. Initially he is poorly treated by most of the staff due to the fact that he uses a cane (he was injured in the Boer War). Thomas Barrow and Sarah O'Brien make several attempts to get rid of him. Despite this, he is eventually able to earn the respect of much of the staff, such as Anna Smith and Mr Carson, who are impressed by his morals and work ethic, despite his disability.
He and Anna grow closer, and she admits that she loves him. He says "he is not a free man". She meets Bates' mother, and from her discovers while in London with Mrs Patmore that he is married to Vera Bates, that he does not love her, that he used to be a drunk and went to prison for a theft that Vera committed.
In 1916, he believes he can divorce Vera and proposes to Anna. However, Vera has learned that Bates has made some money working at Downton Abbey and blackmails him into resigning his job (Robert Crawley is not happy to learn this) against his will and returning to live with her. Anna is heartbroken.
She finds him working in a pub in Kirkbymoorside and convinces him to return to Downton. He offers Vera money to keep quiet about her story that she was blackmailing him with and to leave them alone. However, she is lying. She goes to Sir Richard Carlisle to expose the story, and he pays her for it but does not use it because it would give his then-fiancèe, Lady Mary Crawley, a bad name.
He and Anna marry in a court and spend a night in bed together. No one knows except Lady Mary (she did it for Anna because of her kindness towards Mary) and the maid, Jane Moorsum (Mary claims it is her 'leaving present' to Anna).
Vera commits suicide but leaves behind evidence that makes it look like Bates murdered her. He is arrested in 1919, and he goes on trial for murder. He is sentenced to hanging, but then it is reduced to life in prison.
While he is in prison, Anna comes to see him regularly and Thomas takes over as valet for him at Downton. She gets Audrey Bartlett, Vera's neighbour and closest friend, to give a testimony that eventually proves him innocent. He returns to Downton with Anna and they move to a cottage in the village that is close to the big house so they can still work there. He helps Thomas when Miss O'Brien's scheme ruins his life, showing his true kindness. He, Anna, Joseph Molesley, and Miss O'Brien all travel to Scotland and stay at Duneagle Castle in September 1921. Bates and Anna take a picnic out. They comfort Lady Rose MacClare when she is crying outside and smoking after her mother yells at her. He gives her a mint and she thanks them. Lady Rose teaches Anna to dance at the Ghillies Ball and Bates is pleasantly surprised and says, "Yes. She is marvelous."
John Bates arrives at Downton to replace Mr Watson as valet for Lord Grantham. The majority of staff don't believe that he is qualified for the job, as he has not been a valet before. When it is made obvious that he uses a cane; the staff are at best surprised and at worst outraged; feeling that they will have to pick up the slack for John due to his disability slowing him down in the large house. The job requires him to take the stairs frequently and bring luggage up to people's rooms. Mr Carson is upset that others will need to help him do his job. Meanwhile, footman Thomas was hoping to be promoted to valet himself and is personally offended to lose the job to "Long John Silver".
Most of the staff gives him the cold shoulder, while Thomas and O'Brien try to get rid of him to further their own ends. O'Brien knocks his cane away when he is standing in a receiving line to greet guests arriving. Bates falls flat on his face in front of the Duke of Crowborough. Only the housemaid Anna, who helps him up, offers him any sympathy and friendship. Bowing to the feelings of most of the staff, and as Carson says for the good of the estate, Lord Grantham fires him, even knowing that his friend will have little luck finding another placement because of his disability. But, as Bates is leaving, Grantham runs after the carriage and insists he stay, saying "It's not right."
It is sometime before the rest of the servants learn that Bates is an old friend, and served Lord Grantham in the Boer War as batman. This is where he received his leg injury. Mr. Bates finally says to the astonished and speechless staff with perfect timing, "You never asked."
Throughout the series, he is at odds with Thomas, who tries to get rid of him to take his place as valet. John tries to ignore him at first. Still being ignored by the rest of the staff save Anna, he gains an ally in William when he observes Thomas bullying the younger man who is suffering with severe homesickness. An overconfident Thomas makes a snide remark that Mr. Bates can do nothing to stop him. Bates violently grabs him and shoves him against the wall, showing that despite his disability, he is not to be underestimated - and he has a temper.
John Bates returns to Downton Abbey after his mother's funeral, determined to marry Anna. However his wife, Vera Bates, appears at Downton and blackmails him with the threat to publish Lady Mary's scandal. He returns with her to secure her silence, abruptly leaving service and incurring the ire of Lord Grantham.
Later in the war, Anna discovers that Bates is working at a pub in the village. Both Anna and Lord Grantham visit him there. John reveals he may have information about his wife having an affair, which means he can sue for divorce. However, Vera has compromising information that will delay the divorce.
He goes to confront his wife about this and returns with a scar on his cheek. The next day a telegram arrives informing Bates that Vera has died by eating a pie containing poison. It is suspected that the death was suicide, although lack of a suicide note suggests there was no pre-meditation. Bates had bought some arsenic to kill rats in their house when they were married, and believes that it was her spur of the moment decision to eat the poison. Bates and Anna realize that this looks bad for him and that he may be accused of murdering his wife. She suggests that he go to the police to tell them about the arsenic, as they may find out anyway and it would be worse.
Growing tired of waiting, Anna tells Bates that she wants to marry him immediately. Only Lady Mary Crawley and Jane Moorsum know of the marriage, but the couple planned to tell everyone after the funeral of Lavinia Swire. After attending the funeral, they returned to Downton and discovered two officers who were waiting to arrest Bates for the murder of his wife. Bates and Anna declare their love for each other before he is escorted away by the officers.
John Bates receives the support of Anna, the Downton staff members, and the Crawley family. He is even represented by Lord Grantham's lawyer George Murray. Mrs Hughes, Miss O'Brien, and Lord Grantham all must testify against him. The evidence shows Bates in a bad light and he is found guilty. Although initially sentenced to hang, the lack of apparent premeditation results in commutation to life imprisonment. Anna and the lawyers are still planning to appeal the verdict.Craig to let him be and then he sees Craig being passed something by the guard Durrant. Worried about what he had seen and what he can tell others, Craig planted drugs in Bates's bed, intending to frame him. Fortunately, another prisoner, Dent, who hated Craig, warned him in time. Bates finds the drugs and hides them. But this put him on bad terms with the guards, who cut off all correspondence between him and Anna and prevented her from visiting him.
Dent later told him that Craig and one of the guards, Durrant, were working together selling drugs. Durrant brings them into the prison and Craig sells them to the other inmates. After Bates successfully got Craig on bad terms with the guards by putting the drugs in his bed, his and Anna's letters were finally delivered to each of them. Another guard, Turner, warned Bates that Durrant did not like him and so he became more watchful for an opportunity to deal with Craig. Anna finds information which will clear Bates, Audrey Bartlett saw Vera making the crust for the poisoned pie after Bates had left London by train to return to Downton. As the arsenic was found in the pie, but not the ingredients, Vera had to have put it in herself. Durrant finds out and pressures Audrey Bartlett to change her story when Bates' lawyer George Murray comes to see her. Bates threatens Craig that he will give information to the authorities that will get Craig's sentence extended and Durrant fired, unless they get her to tell the truth.
In 1920, after Audrey Bartlett gave a testimony that cleared his name, Bates was released from prison, and he returned with Anna to a cottage near Downton. They start painting it and it was done by the time O'Brien paid a visit. Mrs. Hughes informs Mr. Bates of the situation regarding Thomas and Jimmy, and though he wants Thomas to go he does not want to see anyone's life ruined. Later he alarms Ms. O'Brien when he mentions "her ladyship's soap," which Thomas had mentioned to him indicating he knows she caused Cora's miscarriage back in 1914. He tells this to Anna as well as his disappointment that Thomas was staying on in a higher position than himself, and he has no idea what the phrase Thomas gave him means.
In 1921, he and Anna travel with the Crawleys to Scotland, and they go on a picnic together. One day while talking outside the house, they meet a crying Lady Rose. They give her sympathy and a mint to hide the fact that she has been smoking. Rose laments her life. With a sad smile Bates tells her that his whole childhood was so bad that she would consider it impossible, but he had survived and so would she. Later, he receives a surprise from his wife at the Ghillies Ball, when she shows how well she can dance, thanks to lessons given to her by Lady Rose MacClare.
After Green rapes Anna during the performance of Dame Nellie Melba, Anna feels soiled and unworthy of her husband. She begins pushing him away, lying that it has been from working too long together which is why she's keeping her distance from him. She even moves back into Downton away from the cottage.John fears he has done something terribly wrong but cannot understand what and that Anna no longer loves him. He cannot learn the truth from her, but after overhearing her speaking to Mrs Hughes he confronts the latter. At first she does not say anything, but then Bates threatens to leave because he cannot work where he is not loved and happy anymore. At that, fearing his departure would break Anna, admits the truth, but insists it was someone who barged in from the outside. However, Bates asks her to swear it was not Green, and she does. Anna too swears Green too was not to blame when John confronts Anna in the boot room. He tells her that she is not soiled, but that he in fact loves her more than ever. They reconcile with embraces and tears, but he is certain Green is responsible, and remarks that he is a "dead man" if it was him. Later, he tells Mrs Hughes nothing is settled.
John swears to punish the man who attacked his wife. He sees himself as having failed to protect Anna. Later, when Lord Grantham goes to America, he takes Thomas Barrow with him instead of John after Mrs Hughes expresses concern that John should stay with Anna. When Green returns with Lord Gillingham, John is listening when Green reveals he went downstairs while Nellie Melba was singing. Later Green dies in London in a traffic accident. Both Anna and Mary suspect John of being involved as he was absent the whole day of the accident, having told Carson he was going to York, but there is no proof he was involved and they take the matter no further.