As soon as Annalise got out on bail, she started to make moves to get justice for herself and find out the truth. She wrote a demand letter addressed to Ingrid Peters seeking a grand jury investigation into an alleged conspiracy launched against her by the District Attorney's Office. She wrote that the letter was a formal complaint and demand to investigate the alleged prosecutorial misconduct by Renee Atwood, listing her unlawful actions including acting on personal bias and false information and orchestrating the disappearance of Wes' body. She hand delivered the demand letter to Ingrid Peters who didn't take her seriously and the two went back and forth, ending Annalise threatens to release what she knows to the press unless the D.A's office finds Wes' body. Later, Bonnie met with Denver and Atwood who were against everything Annalise wrote in her letter. The conversation ended with Denver stating he had files on everybody in Annalise's life. ("It's War")
After it was discovered Denver had the hard drive, he died in a car accident. Nate was determined to find the drive, despite Annalise being worried about the FBI getting to it first. He looked at some case lockers that Denver had accessed when he noticed a case that had been closed for a decade was listed as 'active'. He was able to get the locker opened and found the drive as well as the files. He told Annalise he destroyed them.
Nate began going through the files and discovered that Bonnie had a child that was possibly still alive. He did some investigating - stealing Bonnie's coffee cup and taking it to a DNA lab, stealing a needle someone associated with Julie used and taking it to the DNA lab and having Miller sign off on a release of information form about a missing child stolen from a hospital. His investigating concluded when the DNA on the needle didn't match Bonnie's son, at which point he went to Annalise and told her she needed to tell Bonnie her son was never dead. Annalise told her, and it sent her back to a dark place that she struggled to recover from for a while.
