Emily spent 8 years working at the State Department, and later became a senior partner at Rako (Almost Thirty Years).
Before Season 1
Several years before Sloane's obsession with Milo Rambaldi, Emily's daughter, Jacquelyn, died during childbirth. Both Arvin and Emily were traumatized by the tragedy; Arvin felt abandoned, and Emily preferred to be left alone at times.
To make matters worse, Emily was diagnosed with lymphoma, which she spent all of Season 1 trying to deal with.
Sydney and Jack were invited to have dinner with Arvin and Emily shortly after SD-6 acquired Page 47. While eating, Emily spoke to Will (who Sydney had invited to come along) about the article he wrote in the newspaper about an illegal immigrant living under the rule of a slave driver. Emily told everyone at dinner about the story and how the immigrant led a revolt against the slave driver. The story, ironically, was very similar to the situation Sydney and Arvin were in, foreshadowing that Sydney would lead a revolt against Arvin and SD-6 (Page 47). Later, Sydney visited Emily again to check up on her. They briefly talked about dating and Danny's death before Emily brought up her leukemia. She told Sydney that the doctors could've prevented the disease from becoming malignant if she went to the hospital earlier. The only reason why she didn't go was due to fear of not knowing what she had or how bad it was. Her speech unintentionally led to Sydney having the DSR experiment on her (The Prophecy).
A few months later, Emily was taken to the hospital. Sydney visited her again to cheer up her mood, but when she mentioned work, Emily told her that it didn't matter. She told Sydney that family and friends mattered. During the time, she mentioned that she knew about SD-6 after overhearing some of Arvin's conversations. Unfortunately, the Alliance of Twelve was monitoring Emily's room; it was clear that she needed to be killed (The Solution). That night, Arvin visited Emily herself, knowing that Emily didn't have much time left. She told him that her biopsy was scheduled to happen soon, but it didn't matter; the Alliance would kill her anyway.
After the biopsy, it was revealed that the lymphoma cells in Emily's blood had been decreasing dramatically and that Emily was entering remission. Emily hugged Arvin as she cried tears of joy, unaware that the Alliance intends to kill her (Rendezvous). When Emily was released from the hospital, Arvin sat down with her and confessed that SD-6 wasn't a branch of the CIA. He told her everything without hesitation, and Emily promptly yelled at him and walked away. Realizing the Alliance was going to kill her, Arvin decided to kill her painlessly himself with sodium morphate. During dinner, Arvin poisoned her wine with the substance. After a long silence, Emily told Arvin that she forgave him, and then proceeded to drink the wine (Almost Thirty Years).
After talking to Sydney, Arvin confirmed that Emily had succumbed to her leukemia, and he asked her to speak at Emily's funeral, which she did (The Enemy Walks In). Throughout the rest of the season, Arvin felt like he was haunted by Emily's presence; he kept finding signs and objects about Emily all over his house at night. At one point, Arvin saw Emily walking around in the street (Salvation). It turns out that Emily was still alive; someone put a compound called VTX in her wine, which nullified the effects of sodium morphate. Someone had kidnapped her in an attempt to extort $100,000,000 in bearer bonds from Arvin. After the kidnapper called Arvin, he demanded for him to show proof she was alive. A few days later, Arvin received Emily's severed finger in the mail (Passage, Part 1).
Arvin agreed to go through with the exchange in order to find the kidnapper. But the exchange didn't go as planned; Arvin found pictures of Emily in a newspaper vending machine. She had already been killed (Passage, Part 2).
However, this was all a ruse. Emily was still alive; Arvin orchestrated the whole thing so they could be free from the Alliance forever. She was hiding out in The Philippines; Arvin visited her shortly before the Alliance of Twelve was destroyed (The Getaway).
Arvin and Emily relocated again, this time to a villa in Tuscany. Although Emily was still happy living with Arvin, she became suspicious again after they were forced to flee from the villa. She became even more wary when she realized that Irina Derevko was still alive. Emily questioned Arvin's true motives, but he simply told her that he was "pursuing truth." Fed up with Arvin's lies, Emily turned herself into an American consulate in Florence, agreed to cooperate with the CIA, and demanded to speak with Sydney. When she finally arrived, Emily told Sydney that she only stayed with Arvin because of his devotion for her. She even told her that Arvin admitted everything about the Alliance and that she forgave him. Sydney blatantly told her that Arvin hadn't changed, which was why Emily was at the consulate in the first place. She then agreed to tell the CIA where Arvin was so long as he didn't get the death penalty (Truth Takes Time).
Emily was sent back to the villa, where she agreed to wear a wire so a CIA field team could confirm Arvin's location. Arvin apologized about his obsession with Rambaldi and all of his heinous crimes, but Emily didn't accept it and tried to leave. Arvin suddenly began to tell her that all that mattered was the relationship they had. Guilt-ridden, Emily showed Arvin the wire she was wearing. Surprised (but not angry), Arvin told Emily that he needed to leave, and asked Emily to come with him. She agreed, moments before the CIA stormed the villa. As Emily and Arvin were running over to board the helicopter Sark was piloting, Dixon aimed a sniper rifle at Arvin from the villa, preparing to kill him. Immediately before he fired, a helicopter flew over him and ruined his shot. He hit Emily by mistake, killing her instantly. A sobbing Arvin was forced to leave her body so he could escape, and Sydney and the rest of the team discovered her corpse lying in the grass (Truth Takes Time).
Emily was wed to Arvin Sloane for 30 years. They had one child, Jacquelyn Sloane, who died during childbirth. Emily is not known to have had any other affairs, or romantic relations with any one else, besides Arvin Sloane. Her family members are unknown, but she does have a stepdaughter, Nadia Santos, which she died without knowing. In season 2, Emily fled to a villa with Arvin, then later moved to a villa in Florence, Italy where she was killed. About a half an hour before she was killed, Emily confessed to Arvin that she was helping the CIA and then stated she wanted to leave him. In the end, she decided to join Sloane and take him back, but was then tragically killed by Marcus Dixon.
Arvin Sloane and Emily were wed for thirty years. They had one child, Jacquelyn, who died during childbirth. Arvin did have an affair during their marriage, which resulted in the product of Nadia Santos, who Emily never knew. The couple also faked Emily’s death, so they could escape from the Alliance and hide. Later Emily secretly worked for the CIA for a short period of time and confessed this to Sloane. She stated that she wanted to leave him, but then took him back. She died running along beside him, to escape from the CIA
Relationship with Sydney Bristow
Emily often thought as Sydney Bristow as the daughter she never had, and Sydney often thought of her as a motherly figure. At Emily’s supposed funeral, Sydney gave a speech how Emily was the mother we wish we all had had. Emily also tells Sydney how proud she is for working for the CIA. At the end of season 2, Emily says she know Sydney is disappointed in her for staying on with Sloane. Before Sydney walks away, Emily grabs Sydney’s hand and tells her how much she loves her through the look in her eyes.