As requested via PM, and so others can weigh-in their own interpretations, here is a spoiler-iffic explanation of the Sora Route in Yosuga no Sora as I recall it (haven’t played the game in quite awhile). You have been warned that this is full of major spoilers. So don’t come crying to Narg, if your experience is ruined.
I’m not going to do a moment for moment translation of the story… it’s not my style and would take too long. Instead I’ll outline the major plot points, so that anyone who’s played the game ¬ñ even without knowing Japanese ¬ñ will understand what’s basically going on.
Please excuse any typos. 
EDIT - spoiler tag request
[spoiler]Parent’s Death
Haru and Sora are the children of an upper class family - not rich per se, but well-off enough - whose parents had recently died in a vehicle accident. This is the catalyst that sends the siblings to their grandparent’s home in the countryside (their city apartment was rented; the country house is family owned). It’s these same grandparents that send money to the twins, so they can survive there ¬ñ though it’s somewhat implied they also have access (or are getting access) to an insurance account.
Sora’s Illness
Sora was born with a weak constitution. Even the slightest fever or long term stress can cause her to suffer bouts of near fatal sickness. This condition is incurable, but she takes special medication that alleviates the worst of it. Her condition was worst in her early childhood, as she was absolutely bedridden and could not leave the sanitary confines of a hospital. The nature of the condition is as such, it is unlikely she’ll ever live a life of full independence: when illness strikes, Sora is all but helpless and needs constant supervision.
Kuro Usagi
The black bunny was a gift Haru gave Sora, when she was younger and lived in the hospital. The significance of the bunny is that when Haru gave it to her, that was the moment Sora realized she loved Haru as more than a brother. One has to understand that Sora’s extreme isolation had a profound impact on her relationship with the few people she had contact with. She worshipped her parents and idolized her brother. They were her entire world ¬ñ the reason she lived and lived for. So she fell in love with her brother. For this reason, Sora treasures the doll above almost everything else. This is the reason why she holds on to it, despite being too old for such toys.
Nakanaide Promise
After their parents died, during the funeral service, Sora fell into complete despair. She had lost two pillars in her life. Haru found her crying alone in a corner. It was then that Sora pleaded that Haru never leave her. Haru swore that because they were twins, they shared a bond that made them whole. He would never abandon her, because she was apart of him, just as he was apart of her. This is when he told her, “nakanaide” ¬ñ don’t cry. Thus when Haru says “nakanaide” to Sora (it occurs twice in the Sora route), it is the reaffirmation of his promise to her, that he will always be at her side, no matter what.
Nao Connection (aka why Nao’s scenario should be played first)
While Sora lived her childhood in a hospital, Haru was able to experience a normal one. During these years he met Nao, who grew up as his childhood sweetheart. Before Haru moved away from the countryside to the city ¬ñ in what was supposed to be a permanent move (until the untimely death of his parents) ¬ñ Nao and Haru consummated their love (they had just entered their teens at this time). Sora learned of it. This is why Sora hates Nao above all other women: she is the greatest threat to winning Haru’s heart. Of course Haru and Nao do not realize that Sora knows they had sex, or that Sora has incestuous feelings for her brother, so they are completely alienated by Sora’s total hatred of Nao.
Haru Can’t Swim
Due to a childhood trauma, when submerged in deep water, Haru goes catatonic. Therefore he can’t swim and will drown almost immediately. Sora knows of this…not many else do though.
Okay. With those basics covered: YnS opens with Sora and Haru arriving to the countryside. They encounter Nao on the way. Obviously Haru and Nao are happy – obvious Sora is not. You know why.
Here’s the deal: Haru wants to reestablish the good 'ole days with his childhood friends, when he was having the fun a normal kid would. The problem is that Sora isn’t close with these people: she’s a recluse because of her early childhood… or rather lack of one. All Sora wants is Internet access, junk food, and Haru. No more, no less. Everything else is a complication. They’re Haru’s friends; not Sora’s friends. Haru, wanting Sora to be part of this resurrected life, goes through all the motions of getting her introduced and even having her enrolled in school with him.
Here’s the catch: Sora body can’t handle the life of a normal high school student. She’s weaker and frailer than everyone else. Therefore Haru’s pushing of Sora, leads her to falling ill. Sora not wanting to worry Haru, doesn’t say anything about her failing condition. She gets sick, Haru gets yelled at for pushing Sora too much, and Sora gets dis-enrolled from school to live at home again.
Oh… there’s a major event before this, when Haru gets pushed into the pool by Ryouhei. He didn’t know about Haru’s phobia. Anyways… SPLOOSH!!! So while Haru is drowning/dying, he has a flashback with his promise to Sora about never leaving her. So on the verge of death, he slowly revives, hearing his emotionally distraught sister calling his name, begging him not to leave her. He doesn’t of course, and as soon as he revives, the first words that leaves his lips are, “nakanaide,” which mentioned previously ¬ñ has huge significance for the twins. It’s after this drowning scene, that Sora makes the determination to have no regrets and pursue a romantic relationship with Haru.
Now moving forward, back to after Sora got sick from school life, Haru stays home a lot to watch Sora, because he almost lost her too¬Ö he also realizes that he’s being selfish and forcing Sora to live the life he wants (not what she wants), which is dangerous to Sora’s health. This leads to that, Haru knows about Sora’s incestuous feelings, and next thing ya know: Haru is banging his own sister¬Ö okay¬Ö it’s not really that simple, but you get the picture.
So then, after a few weeks of this, Nao and friends catch Sora and Haru in the act ¬ñ and it doesn’t help that Sora is practically bragging about it. So obviously, things go totally downhill from there. Haru ¬ñ being a social person ¬ñ is emotionally devastated, and hides from everyone due to absolute embarrassment of the taboo. Sora ¬ñ only wanting Haru and nothing else ¬ñ is alienated by Haru rejecting and ignoring her at every turn. Essentially Haru’s life is destroyed.
Little bit of this, little bit of that, Sora comes to the realization that she’s the reason for Haru’s problems. Doesn’t help that Nao is rubbing it in as a tit-for-tat. Haru had a childhood: Sora did not. Haru had friends: Sora did not. Haru could live a normal life: Sora cannot. So Sora plans to kill herself, because she’s what’s holding Haru down. Haru can live without her; she can’t live without him.
Haru shakes out of his self depression, after realizing Sora doesn’t bother him anymore, and goes looking for her: discovering that Sora decides to drown herself. Haru tries to intervene, Sora tells him to get back, Haru ignores her and keeps wading deeper into the water to get her. His catatonia kicks in, and Haru drowns. Sora saves his ass. We get a slight repeat of the pool drowning event: including the whole nakanaide promise¬Ö this time with Sora promising not to leave Haru.
Epilogue is about Sora and Haru leaving the country, to restart anew. Nao and the gang accept that Sora and Haru are perfect for each other, and hope them the best from afar. Basically it came down to two choices: Haru had to pick between living a life with his childhood friends or living a life with Sora. Because of Sora’s nature and condition, it was unreasonable for both. He decided on Sora.
Ryouhei inherits the harem. 
Some extra points to mention:
Sora and Haru Connection
Haru is exceptionally healthy and fit, even though he doesn’t put much effort in staying so. There’s a morbid allusions that Haru “stole” the “health” from Sora in the womb. So at Sora’s expense, Haru is so healthy. Haru obviously has a bit of a guilt trip on this.
Haru Goes with the Flow
Haru isn’t a spineless wimp, but he lacks strong will to do what he wants for himself or go against others. Haru is the kind of guy, who lets the current take him places, rather than pick the destination. This is apparent in explaining the Nao romance, through the Sora route. It’s not to say that Haru disliked Nao, but that Haru had sex with Nao, because Nao wanted him too. Haru accepted the current. This personality flaw is likely what led him to having sex with his own sister.
Haru is as Selfish as Sora
Not as direct about it; but he’s a total ass in his own way.[/spoiler]