Something I don't think a lot of people realize about Nugget and Lily's relationship is that they're actually a lot more closely intertwined than it would initially appear.
In the first game they are the ones who were the closest to Billy and were clearly the most affected by his disappearance. Lily making it her goal to find him no matter the cost and refusing to make friends or really even socialize until she's done. Meanwhile Nugget became grief-stricken by Billy's disappearance to the point where he began taking the principal's pills just so he could forget the pain.
Lily and Nugget are also the ones who end up being targetted by the two major bully characters in the first game, with Cindy's mission revolving around humiliating Lily while Nugget has slop thrown at him every morning by Buggs.
Nugget and Lily's missions also have pretty close ties to each other, with Nugget's mission requiring the player give Lily a love letter while Lily's mission is only accessible if you give her Billy's note which Nugget gave to you and also requires the player to be sent to the principal's office by Nugget, so even if he's not directly involved he is still incredibly important to the mission.
Last thing I want to point out about the first game specifically is that Lily and Nugget are both portrayed as outcasts of sorts. Nugget is self-explanatory with how he admits to having no friends and the fact that everyone (including Lily) finds him weird, but Lily herself doesn't really seem to be in a much better position.
She has no friends outside of Billy in the first game. No one even talks about her outside of Nugget, Cindy, Jerome's dad and Ms. Applegate, and of those four only one of them actually sees her in a positive light, everyone else either hates or ignores her.
There's admittedly not as much to say about their relationship in the second game as they literally have no interactions outside of Creature Feature due to Lily being in hiding the whole time. That said I do find it interesting how it is Nugget specifically that she decides to give the Monstermon Plush to when it probably would've made more sense to give it to Kid considering he was the one who helped her save Billy in the first place, yet it was Nugget who she ultimately trusted it with at the end.
Aside from that there is the other, more obvious stuff, like Nugget's mission once again being crucial to her and Billy's, the fact that Nugget actually plays a direct role in said mission and of course, the ship tease moments at the end of the game.
Finally there's Kindergarten 3. I doubt I even need to explain this one. Nugget and Lily literally get their own mission together that is all about exploring their relationship dynamic, do I really need to explain myself here?
Outside of these specific instances, there are also other ties they have that aren't tied to any specific entry and can be applied to the entire series.
Lily and Billy's dad is the one who created the Monstermon Cards which are required to get the secret endings of the first two games where Nugget fucking murders everyone.
Both Nugget and Lily are named after and have a strong associations with an inanimate object (Nugget being well... nuggets and Lily being flowers)
I'm sure there are more details that I'm missing here, in which case feel free to point them out. But my point is that Nugget and Lily's relationship goes way deeper than just "weird kid likes pretty girl and pretty girl might like him back". They are both crucial to each other's development and have ended up driving out each other's best qualities because of it.
Had it not been for you giving Lily Billy's note at the start of her mission (something which Nugget says you should do by the way), Lily would've never found her brother and she would've remained the sad, lonely little girl that no one pays attention to unless it was to bully her. Instead she did find him, and we can see in the latter two games that she's much more confident and sure of herself than she ever was in the first game. All I'm saying is that Lily post-Kindergarten 1 would not have taken Cindy's bullshit and you can at least partially thank Nugget for that.
As for Nugget himself, while his development is a lot more subtle than Lily's is, he is shown to be a lot friendlier and more heroic in the second and third games compared to the first. He still does a lot of morally questionable things but it does appear that spending time with Lily has genuinely made him a less murderous person, even if he still dabbles in violent acts occasionally.
Overall, the point of me making this post is to say that Lily and Nugget's relationship is a lot more interesting than first meets the eye. I'm not saying that you have to ship them or anything, it's fine if you don't, I just made this post cause I love these two goobers and think they deserve more love.
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