Why Abby Sciuto Left the 'NCIS' Team

After 16 years and over 350 episodes, fans finally said goodbye to Abby Sciuto (Pauley Perrette) on NCIS Tuesday. While she didn't leave the show in a body bag like many viewers initially suspected, there still may be some confusion surrounding why she left. (Major spoilers ahead!)

After the cliffhanger ending from last week's episode ("One Step Forward"), many fans assumed the gunshot and cut to black during the apparent mugging with Clay Reeves (Duane Henry) meant Abby would be dead come Tuesday night during "Two Steps Back." But the episode wasted no time in revealing that Reeves was the one in the body bag, after joining the team just last season.

Meanwhile, Abby was in critical condition, with viewers seeing several flashbacks throughout the emotional hour — including a surprise phone call from Tony DiNozzo (Michael Weatherly), who left the team in season 13.

After investigating the mugger, who wound up being a dishonorably discharged Army specialist, the NCIS team discovered it wasn't a random attack; it was a hit on Abby's life. As it turns out, the hit was ordered by Marine Sergeant Robert King (Peter Jason), the black-ops soldier who tricked Abby into developing a bio-weapon back in season 6.

Fortunately, Abby woke up halfway through the episode and decided to confront King on her own. She slips cyanide into King's coffee and tells him, "Kate. Jenny. Dorneget. Ziva. Reeves. I am tired of my hero friends dying while villains like you get to live." She offers to save his life if he confessed to ordering Clay's death. "Sometimes you have to get your hands dirty to get the job done," she said. And that she did, having actually spiked his coffee with extra caffeine.

But Abby left NCIS for a reason bigger than that; she told the team she was going to arrange Reeves' funeral plans to be buried next to his mother in London and then repay Reeves the debt she felt she owed him.

"I'm not coming back. I'm leaving NCIS," Abby said. "Clay died saving my life and I owe him a debt and I tend to see that through. Clay always wanted to start a charity in honor of his mom and since he's not here to make that happen, I will. I know you may not understand, but it's something I have to do, not just for him, for me."

She continued, "It wasn't an easy decision. You guys are my family and this is my home, but you have to go with your gut and my gut is telling me that I have to go."

"It's not goodbye for good," she said to McGee, who said he couldn't say goodbye to her. "It's goodbye for now."

Instead of an in-person goodbye with Gibbs (Mark Harmon), Abby left him a note.

"Hey, Gibbs. You're probably wondering what's with the retro communication. Truth is, I chickened out. I was afraid that if you asked me to stay, I might waiver because there's nothing I wouldn't do for you," Abby's note read. "When I think back on when things in my life got difficult you were always there to tell me that it would be okay. And it would be because you would make it okay. But Gibbs, Reeves is gone and it's not something anyone can fix. Not even you. I hope you know what you mean to me, Gibbs. Every moment, every lesson, every hug. I'm thankful for it all. No matter what we faced over the years, there was only ever one thing I needed to hear from you."

As Gibbs looked out his window, Abby was standing there, leaving him to sign to her that he loved her.

Abby's exit comes after months of speculation about how the show would send her off and why she was leaving. While we now know why Abby left the NCIS team, many are still wondering why Perrette made the decision to leave the show. She blasted rumors last fall that she was leaving to pursue a skin care brand or due to disagreements with CBS, and in recent interviews has alluded to the idea that she simply wants more privacy.

"It's being a commodity," Perrette told CBS News. "I think I've earned some time to myself (to) stay home, go to church."