The novel has two endings, the first of which is a bummer, and the second of which is a bummer with a silver lining. That's the best we're going to get, folks.
Ultimately—spoiler alert—Will decides to go through with his assisted suicide. Lou is furious when she learns this—especially because it comes right after her declaration of love for him—but she eventually relents and accompanies him to Dignitas despite the protestations of her mother. This is a big moment on two levels: it shows that Lou is willing to be there for Will even if she disagrees with his decision, and it also shows that Lou is not going to let her family control her actions as they always have.
The epilogue finds Lou in a Paris café, which brings to mind a conversation she had with Will earlier in the novel, when Will told her that Paris was his favorite place on the planet. And it turns out that Will directly requested that Lou go to Paris: he gave her a letter saying that it should only be opened in a Paris café, accompanied by coffee and croissants. He wants to make her start really living her life.
The letter covers a lot of stuff, but the gist is that Will knows that Lou will be a better person for their relationship, even if it causes her pain right now. To that end, he leaves her a small amount of money that will allow her to fund her schooling.
In the closing moment of the novel, Lou gets up and heads "off down the street toward the parfumerie and the whole of Paris and beyond" (e.32). This represents the most important way that Will has changed Lou: she is now eager to explore the world without letting fear control her. That's a priceless gift.