Francisco Vargas' Assassination is one of the main storylines in season six of Scandal.
It is later discovered that Rowan was ordered to assassinate Francisco by Samantha Ruland and Theodore Peus, they blackmailed him by kidnapping and threatening to kill his Highschool sweetheart and girlfriend at the time Sandra Potter, Rowan ended up killing Sandra (shooting her between the eyes) to save her, not knowing that Peus already had a target on his daughter Olivia Pope. Peus and Ruland also ordered Meg to assassinate Jennifer Fields, she was the only one alive that knew about the assassination.
During the Mellie's Inauguration Olivia Pope's Mother has her sniper rifle aimed into the crowd and tells her daughter to move out of the way so she doesn't kill her. Maya Lewis is shot down before she can take the shot but Olivia Pope is determined to find out who she was trying to assassinate. Later, at Olivia Pope & Associates the team look at the seating for the Inauguration and realised it has been changed, they watch the tape of Francisco Vargas' Assassination and realise that both of these event has one thing in common, Luna Vargas.
With a lot of persuasion by Olivia Pope and Jake Ballard, Luna Vargas confesses and tells them both that she hired Theodore Peus, Samantha Ruland and Meg to make sure her husband Frankie Vargas lost the election and didn't become President because she didn't want to be trapped in the life of a First Lady when her husband took the Oval. She also claims that Frankie would have had to "compromise" himself too much and not get anything done whereas she could have accomplished so much ("imagine what Jackie Kennedy could have done as President after Dallas"). She's forced to kill herself to avoid the shame of the trial ruining her children.