Gretchen was introduced via a flashback. As Walt and Jesse Pinkman are cleaning up the liquefied remains of Emilio Koyama's corpse, Walt reflects to a moment back in his college days where he and Gretchen, alone in a dimly-lit classroom, attempt to inventory the chemical makeup of the human body with exact percentages. When their total falls 0.111958% short of 100%, Gretchen posits the possibility of a soul ("...and the Bag's in the River").
Walt and Skyler White go to Elliott's birthday party, where they meet him and Gretchen for the first time in ages. Elliott, who is exceptionally wealthy thanks to Gray Matter, offers to pay for Walt to receive the best cancer treatment from Dr. Delcavoli. Afterwards Gretchen urges Walt to take the money, but he lies by saying they won't require financial help because their insurance will cover it ("Gray Matter").
Gretchen later discovers that Walter lied to his family about her and Elliott paying for his treatment, horrified when Walter angrily and bitterly blames her and Elliott for ruining his life. Although she claims that Walter sees it wrong, it is still unknown what transpired, only that on Fourth of July weekend with Gretchen, her father, and her brothers, Walt was in his room packing his bags and barely talking. Walt left Gretchen and his research behind suddenly and without explanation. Although Gretchen still keeps Walter's secret, she later tells Skyler that she and Elliott will stop paying for the "treatment" ("Peekaboo").
Later, after Skyler's suspicions of Walt having an affair with Gretchen is renewed, Skyler makes contact with her and Gretchen eventually tells her that they never paid for any of Walt's medical bills. ("ABQ")
After his life crumbled apart, Walter is at a bar in New Hampshire when he notices on the television that Elliot and Gretchen are being interviewed by Charlie Rose. The talk about their recent donation of $28 million to drug rehab clinics in the American Southwest, and Charlie questions if this has any ties with the revelation of one of the co-founders of the company being the infamous Heisenberg. Gretchen and Elliot tell on live television that Walt had absolutely nothing to do with anything ever accomplished by Gray Matter except for the idea for the company name, prompting Walt to become extremely angry and change his mind about allowing himself to be captured by the police in the New Hampshire tavern. ("Granite State")
When Walt returns to Albuquerque to tie up loose ends, he pays a visit to Elliot and Gretchen at their new home. She and Elliot help Walt bring in his money, and Walt explains to him that they will give his children his money in the form of an irrevocable trust on Walt Jr's 18th birthday. He explains to them that his wife and son both hate him and would never accept his money, and even if they did the federal government would never let them keep it. However, it would be accepted if it came from two rich benefactors who are generous enough to write a $28 million check to support victims of Methamphetamine abuse. It also makes sense since, according to Walt, "My children are both blameless victims of their 'monstrous' father, a man that you once knew quite well." After they shake hands with Walt to confirm the deal, what appear to be two red lights from sniper rifles come out of nowhere. Walt warns them that if his children do not receive his money for any reason, a sort of "countdown" will begin that may take place anywhere and at any time. As Walt leaves, Gretchen collapses in tears, left to contemplate her fate as well as the monster that Walt has become ("Felina").
- Walter: "I don't know. Just...doesn't it seem like...something's missing?"
- Gretchen: "What about the soul?"
- Walter: "The soul? There's nothing but chemistry here."
- —Walt and Gretchen in their earlier years.[src]
- Gretchen: "Let me just get this straight: Elliott and I offered to pay for your treatment, no strings attached - an offer which still stands by the way - and you turn us down out of pride, whatever. And then you tell your wife that in fact we are paying for your treatment. Without our knowledge, against our will, you involve us in your lie, and you sit here and tell me that that is none of my business?"
- Walter: "Yeah. That's pretty much the size of it."
- —Walt and Gretchen.[src]