- Logan – Tell me not to get on that plane. Tell me to blow off my father, the paper, the whole Huntzberger destiny. Just tell me I can figure something else out. Just tell me not to go
- Rory – Well, I can't do that
- ―No support[src]
When the show returned 9+ years later, Rory and Logan are having a "Vegas" type affair. In spite of the fact that he's engaged and she's in a two-year relationship of her own.
Logan and Rory first meet when Logan and his friends pass by Rory and her friend Marty and Logan and his friends tease Marty and pay little attention to Rory. However, when Logan meets Rory for the first time in the hall he is captivated by her debate skills when she gives him a good lecture about how he treated Marty. Logan continues to debate with her and promises that he will always remember Rory. Rory at first thinks Logan is just a lazy rich boy, the kind of boy Lorelai has warned her about. However, slowly she changes her mind when she needs help on a article of a secret society that Logan is in called the Life and Death Brigade, she is fascinated by the club and is convinced to take a dangerous jump with Logan causing Rory to look at Logan in a new light. Logan also comforts Rory at a party after she and Dean break up.
Rory soon has a crush on Logan, and while Logan admits he likes her as well he says he is not a commitment guy so they agree to a no strings relationship. During that relationship there are signs that they both want more like when Logan is jealous of Rory dating his friend Robert, Rory eventually decides the relationship is too much for her so she tries to end it. However, Logan, not wanting to lose Rory and caring about her more than any other girl, agrees to a monogamous relationship. Despite the disapproval of his family and Rory dropping out of Yale, their relationship is stable until a break up in S6, though Rory doesn't think of it as a break up. Logan was threatened by the arrival of Jess in Season 6, even more so when he found out that Jess and Rory had been "high school sweethearts", and acted a little bit like Jess in comparison to Dean. After Rory argued with Logan about his behavior towards Jess and the aimlessness of their life together, they decided to "take a break". However, Logan saw this as a break up and proceeded to sleep with his older sister's friends for comfort.
Logan is also known for making grand and romantic gestures, usually as an apology, such as purchasing a coffee cart and barista for Rory's own personal use. Rory loved the gifts but didn't give in until Logan swallowed his pride and went to Lorelai for help. He convinced Lorelai that they both had something in common because they hated Mitchum and Lorelai was impressed by Logan's moxie. Lorelai wrote a letter and Rory agreed to give Logan another chance. Logan proved himself even worthy more when he and Rory save the Newspaper under Paris's tyrannical reign. Rory and Logan have a good relationship and they even move in together after Paris's kicks Rory out of their apartment. They also go to Martha's Vineyard with Luke and Lorelai; and Luke looks at him in a new light when he helps Luke with a Valentine's gift. All is well until Rory found out that he had slept with his sister's friends just before Honor's wedding, which causes a more serious rupture.
The rupture ends when Rory realizes that she can't get back at him with Jess because she still loves Logan, and it improves even more when Rory takes care of him after a base jumping accident in Costa Rica involving the Life and Death Brigade. At the end of Season 6, he is sent to London by his father to take charge of his family's business and, according to Mitchum, "set him on a path". Season 7 sees him acquiring an interest and penchant for his work (in London, then in New York), despite the distance Rory and Logan's relationship continues to grow. Logan surprises Rory with a moonlight picnic on the roof and even though Logan has a attractive co-worker in London he remains faithful.
Rory and Logan's relationship remains sturdy despite two small dramas. The first being when Rory writes an article about the people at Logan's business launch party, and Logan doesn't like the way they're described, because they're all like him. The situation ends up fairly nasty- with Logan bringing up the fact that Rory isn't exactly different, and Rory walks out of their apartment. The pair soon make up. The other being when Logan gets jealous because Rory tells him about Marty's old crush on her, and doesn't think it is right that Rory and Marty are lying to Lucy, Marty's girlfriend. This results in Logan bringing up the fact the pair are lying at a dinner they all have together, causing Lucy to stop talking to Rory.
Despite the outburst, Rory spends Christmas with Logan in London, as the couple planned. Rory gushes about it with her Mum, and says that although Lucy still won't speak to her, Logan and her are back on track together.
Logan is there for Rory when Richard has a heart attack he borrows a chopper and rushes to her side. He also tells Rory that he has trust in her when Rory admits she has a crush on a T.A.
Later, after getting involved in a bad business venture that brings a lawsuit in Season 7, which causes some tension between Logan and Rory until Logan quits working for his father and Logan apologizes to Rory for neglecting her and work. They go to Stars Hollow and Lorelai finally begins to accept them. Logan asks Lorelai's permission to ask Rory to marry him. Logan proposes to Rory one episode later, but Rory asks for more time to think. Logan makes the offer one last time in the penultimate episode, at Rory's graduation from Yale, saying it's all or nothing. Rory still turns him down saying that even though she loves him she wants a wide-open future, and Logan takes the ring back, and walks off. Logan does not make an appearance in the final episode, Rory says she hasn't talked to him and the pain comes in waves.