What happened to Sakura? In the Visual Novel of Fate Stay Night, both Fate and Unlimited Blade Works routes share the same start with Sakura making breakfast for Shirou and Shirou seeing her in the Archery Club. 

If Unlimited Blade Works is completed, during these initial days, at one of the times where Sakura is preparing breakfast for Shirou, the player can select to notice a bruise Sakura has, netting the player some of the critical affection points with her to go into the Heaven's Feel Route. (We can assume it was Shinji who gave Sakura that bruise).

In Heaven's Feel, after Rider was defeated early Shinji's tome burned up, later when Blood Fort Andromeda is activated we find out that Sakura is Rider's true Master and Shinji got a second book from Sakura who gave him the books because didn't want to participate in the war (Shinji was begging for Sakura to make another book, and warned her that if she were to participate, she would have to fight Shirou). We also find out about Sakura's connection to the Greater Grail later on in the route.

We know Shinji is killed by Illya and Beserker in Fate, and in the Unlimited Blade Works, he was only defeated and went to Kotomine afterwards. However, I am wondering, what happens to Sakura in the Fate and Unlimited Blade Works routes?

I am looking for a canon explanation. I don't believe the events in the Studio DEEN's adaptation of the Fate Route are canon, as the showdown between Rin and Sakura is actually a throw back to Heaven's Feel. Not to mention the whole arc (Caster trying to summon the Grail) is an arc in the Unlimited Blade Works route (in the original Fate Route, Caster appears briefly near the end, but is killed by Gilgamesh's Gate of Babylon.
Fate/hollow ataraxia is the official sequel to Fate/stay night. It has radically different feeling to it, bringing more comical relief and tongue-in-cheek references, but it's as close to "canon" as we can get. It doesn't follow any particular route from F/SN.

I didn't read F/HA, but here's how TYPE-MOON Wiki references Sakura's development:


  In Fate/hollow ataraxia, Sakura lives a peaceful life in Fuyuki City,
  which Rin has left in Sakura's care while she is at the Mage's
  Association, and Rider comments that Sakura is now the popular new
  captain of the school archery club. Sakura's dark side still exists,
  but appears only for comic relief. Shinji reveals to Shirou that
  Sakura assumed control of the Matou household, and both he and Zouken
  are terrified of her.
  
  In the eclipse story The backside of Kibisis Rider and Sakura seem to
  work together to seduce Shirou and engage in a threesome with him.
  Actually this is all Rider's doing, trying to get Shirou to pursue
  Sakura more aggressively. Yet in the middle, Shirou realizes the truth
  and reverses her spell on her, in the end revealing to viewers that
  Rider herself has deep feelings for Shirou. Sakura appearing in this
  episode is only a conjecture by Rider's spell, a representation of
  Rider's true intentions of her actions.


There doesn't seem to be any canonical explanation beyond this. Personally, I think it's part of why people like Heaven's Feel so much: the thought of Sakura undergoing torments under Zouken until she dies just doesn't feel right.