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Thunderstorms and Sakura Blossoms
Thunderstorms and Sakura Blossoms by Lady Silq Ice
The final battle leaves little behind, how are two souls to recover from such loss? WARNING Character deaths and lemons. Complete.
Rating: MA - Universe: Canon - Status: Complete - Category: Chapter Stories - Genre: Action, Angst, Drama, Friendship, Humor, Romance, Tragedy - Updated: 11-10-11 - Created: 07-13-09 Chapters: 42 - Reviews: 26 - Words: 181,460 - Reads: 74,352 - Anonymous Reading: Yes
I just finished re-reading this one, which is why your description triggered this one. If this is it, then the part you are remembering happens about halfway through the story: Kagome is visiting an old shrine as part of a university research project and is kneeling on a memorial stone praying that she can get back to the past - to Sesshomaru - when she is transported back and dropped mid-battle.
ETA: No YIMs!