Ash and Pikachu are involved in a horrible accident. To preserve Pikachu's life, Ash calls his friend into it's Pokeball. Almost lifeless, Pikachu succumbs.
Ash and Pikachu's Pokeball were never recovered.

500 years into the future Ash's body and Pika's Pokeball are unearthed during a archeological dig. The scientist know what Pokeball and pokemon are.
As a research tool they are able to transfer the mind of a pokemon into the empty shell body of a human clone. To learn more the scientist use this method on Pikachu.

The body they choose is that of a young Caucasian girl. Long blonde hair, blue eyes.
With some rehabilitation and some social lessons, the scientist teach HumanGirlChu how communicate in the new dialect while HumanChu does the same from it's memories if it's time.

A small amount of time passes and HumanChu learns much from the modern day society also learning of a new time-traveling technology. HumanChu, still having vivid memories and feelings of longing for it's ancient trainer, Ash, decides to look into the rumour. She investigates and has an opportunity to unofficially use it, and does.

The time-tech throws her back into the past.
The time-tech is un-tested and new and it sends her back but not exactly when or where she wanted. The exposure to the time stream retro-grades her body into that of a younger version and she is not sent to, where Ash died and she got trapped and in slightly earlier time period.

And you know the rest of the story... until

HumanChu, CANNOT use the time-tech to tavel back, nor wants to, so stays and decides to be around to save Ash. Along the path and coming up to the incident, another time traveler comes back to explain to HumanChu that saving Ash will not work. If she saves Ash and Pikachu, she will no longer exist, therefore unable to be around in the future to start the process.

So HumanChu implements a plan, She convinces Ash to bury himself and Pikachu, when they die, in the exact location when they die.