If during the two years between 699 and The Last, Naruto and Hinata are shown to have grown to be closer friends. They form a deeper friendship and share laughs and experiences with each other. Naruto and Hinata are comfortable in each other's presence and really know each other, instead of the horribly pre-genin like dynamic between them. Naruto is confronted by Sakura on why he hasn't answered Hinata's confession to which he replies that he didn't feel the same way and didn't want to hurt her feelings. When asked if he still feels that way, he responds that he isn't really sure anymore. Hinata is planning to give Naruto a scarf and finally bring up her confession/the feelings she sill has for him, so she can get a definitive answer.

When she tries to give it to him initially, the village is attacked by the moon people (lel Kishi what have you done to your series) and Hanabi is kidnapped by Toneri during the fight. Distraught and worried, she momentarily forgets about confessing and personally asks Kakashi to be on the team to go after her. Naruto, wanting to help his now close friend in any way, asks to come along. During the mission Naruto and Hinata bond over Hyuugaa stuff while keeping on task with the mission, and Naruto is impressed by how much her ninja prowess has grown. Naruto begins to recognize that he may be feeling something other than friendship toward her, and urged by Sakura/Sai/whoever the kitten, gets teh mind to tell her. Hinata has been cornered alone and given an ultimatum, to switch her sister, unharmed, for her. When Naruto sees Hinata leave camp late at night, he follows her, only to find that she is meeting with Toneri. Hinata tells him not to try and stop her, and Toneri flies off somewhere or whatever they have him do, leaving Hanabi's unconcious body and a distraught and confused Naruto. 

Taking Hanabi back to the rest of the team, he informs them of what's happened. Initally, the rest of the team want to regropu back at Konoha, but Hanabi and Naruto stay adament that they should go after her (unlike Naruto's heavily uncharacteristic reaction to just give up as if her leaving terms weren't extremely shoddy coupled with the fact that they still need to defeat Toneri regardless). Hanabi, who has been paying attention to marks to tell where Toneri's hideout is, leads the way. They find and defeat Toneri, yada yada, and during the final blow, Naruto declared his feelings to her. Hinata responds the same, and they leave together with the rest of the team and have that moonlit kiss (dropping the scene with them running together, as it implies that they have always been together/have gone through the years by each other's side and that is not the nature of their relationship and is an out of place scene).

That's pretty much how any half decent writing could have done it. But this is SP