Under Tom Kirkman’s authority, Hannah became the lead investigator into the terrorist attack that killed everyone present at the Capitol (with the exception of Peter MacLeish, as was discovered later). 
During the events of the first season, Hannah was the one to eventually find that Peter MacLeish, the survivor of the Capitol bombing, was hiding in a bomb shelter beneath the Capitol and that he was involved with the conspirators responsible. She also discovered the identity of another conspirator, named Catalan. Ultimately, she was able to expose the conspirators who dubbed themselves as the True Believers and thus led to their downfall.
She worked on an investigation into Andrea Frost, who she thought to be the hacker known as, "Gamine," that was responsible for hacks into NASA, the Power Grid of Washington D.C, President Kirkmans therapy tapes, and other hacks, which resulted into multiple deaths including Damian Rennet. She had publicly humiliated Andrea Frost by accusing her of these actions and sabotage against President Kirkman, after the president told her to find concrete evidence and Frost admitting to a private conversation at the Cabinet hearing against Kirkmans mental ability to remain in office. After the fact, these actions seemed to have gotten Hannah fired by President Kirkman in the Oval Office.
However, the firing was just a setup since the model car in the office was bugged by Kirkman's close friend Dax Minter, also known as Gamine. Without going too deep, Hannah Wells was not fired. In the end, Aaron Shore and Hannah Wells were together at a bar when Hannah Wells pulled out her White House ID and her FBI badge and laid them next to him, signifying her resignation.
At the end of Season 2, Hannah arrived in England to search for Damien's daughter Amy. While there Hannah killed Valeria and at Amy's behest, brought her back to American. The season ends with Hannah watching a video obtained from Valeria which contained a scene where Emily Rhodes hands some documents to Valeria.
In Season 3 Hannah is recruited by the CIA. During her bioterror investigation, she eventually discovers a hidden biolab in a brewery. She dies from the poisonous gas produced in the brewery.
A few moments after the Capitol explosion, Hannah made an attempt to call her partner, Scott Wheeler who was a member of Congress that died in the Capitol bombing, but was sent to voicemail. After seeing the plumes of smoke rising from the Capitol in the distance, Hannah got in her car and drove to the flaming wreckage. While the FBI and emergency services dig through the rubble, they find an explosive commonly found in the Middle East, but was later deemed dysfunctional. From that point, most of the team suspected major terrorist groups in the Middle East, but Hannah became skeptical. She theorized that whoever perpetrated the bombing was just getting started.
Dead in the Year 2020.