When Rory wakes up after Logan has gone to London, she finds he left her a model rocket ship as a gift (ep. 7.01). She pretends she understands the reference, but only later finds out that it's a reference to an old Twilight Zone episode, called The Long Morrow (also the title of this episode). The rocket ship is symbolic because it's about a man waiting his whole life for someone, as he was going to wait for her while in London.
When Logan calls to see if she likes the gift, she pretends that she understands the reference but she, along with Lorelai, are utterly confused. Rory ends up spending the whole day researching into rockets on the internet until she finally stumbles upon someone in a forum who recognizes the rocket, informing her of the exact reference and Rory soon adores it.
As it turns out, the rocket refers to a past moment in their relationship (which has not been depicted on the show) where she and Logan are watching an episode of The Twilight Zone from 1964 called 'The Long Morrow'. The episode is about an astronaut named Douglas Stansfield who is sent on a space expedition 114 light years from Earth which will take 40 years. However, prior to that, he falls in love with a woman named Sandra Horn but is distressed that when he returns, she will be 40 years older, and he will remain the same due to him being in suspended animation for the trip. He leaves tragically for the expedition, heartbroken, but it's revealed that during the trip, he turned off the suspended animation to be the same age as Sandra, unaware that Sandra has put herself in suspended animation to remain youthful with him.
This gets through to Logan as the man willingly wasted 40 years of his life to become a 80 year old man just to spend his last few years with Sandra to which Logan comments, "That's true love". The episode is Logan's favorite episode of the series and Rory now completely understands that Logan gave her the rocket to let her know she is his true love and that regardless how far apart they are, he will always wait for her, to which she gleefully adores and swoons about to Lorelai after much research on Logan's mysterious gift.
Strangely enough, even after their break-up shortly after Rory's graduation, the rocket can still be seen in Rory's possession, giving hope to fans of the couple that Logan wasn't the only one who believed their relationship was true love.