Legend has it that when a world has gone through a thousand cycles of reincarnation, the hopes and wishes of its people can change the course of its original timeline. I call this a "miracle."
In the year 1522 of the Sea Circle Calendar, after the shipwrights of Water 7 had declared the Going Merry unable to sail, it forced itself to keep going and rescued every member of the Straw Hat Pirates before splitting in two on the open sea.
Afterward, Luffy gave the Going Merry a burial. Engulfed in flames, it bade farewell to Luffy and the others, then sank beneath the sea and fell into eternal slumber.
The transmigrated Merry inherited the Going Merry's memories and last wish, and continued accompanying the Straw Hat Pirates on their adventures.
