So Sweetie somehow wound up in Equestria: Total War, and the other two went into Lost Time?
 
Captain Hero Bloom: …Sucks to be you!

From the source:
 
The Cutie Mark Crusaders are transported 100 years into the future (maybe by Dr. Whooves, one of Twilight’s spells gone wrong, through their own recklessness etc.). They each are teleported to a different location in space as well, meaning they enter this future Equestria each on their own. Within a month, Apple Bloom and Scootaloo find each other, and travel together to Ponyville, determined to find Sweetie Belle. When they discover that Sweetie Belle is not there, they search far and wide to find her. A year passes, and their hope of finding their friend is diminishing. The two return to Ponyville with heavy hearts. It is shortly after this that they run into an extatic white filly, with tales to tell of surviving in a dangerous land at war with itself.

@RIG  
Based upon Sweetie Belle’s look, I’d say it’s one of those ‘we thought you were dead’ situations.

why are they crying? what happened?