>Human enters Equestria and can't return home (Question 1: Aside from death or magic, how?).
>Human manages to get a job somewhere (Question 2: Which known city: Ponyville, Canterlot, Manehattan, or Crystal Empire?)
>Human finds himself interacting frequently with Pony 1.
>Eventually, Pony 1 becomes interested in human, but human is oblivious.
>Pony 1 starts stalking as s/he becomes obsessed with human.
>Human meets up with Pony 2, who is friendly but not interested.
>Pony 2 is actually interested in Pony 1, much in the same way Pony 1 is interested in the human.
>One relationship succeeds, two relationships fail - one nicely and the other tragically.

Question 3: Who are Pony 1 and Pony 2, if neither can be Lyra, Pinkie, or Twilight?

2924366 worm hole, Ponyville, Daisy, Bon Bon

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Updated; answers may be changed.

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Answer one: Lab Test. (Never leave a janitor alone in a lab full of equipment he/she may not understand... or alternatively, he/she may have volunteered to be tested and something goes wrong.)

Answer two A: Canterlot
Answer two B-C:Ponyville
Answer two D: Manehattan

Answer three A:Fancy Pants and Fleur De Lis. Choose which one is pony 1 and Pony 2 on if the human is male or female... or if you want the story to swing one way or the other.

Answer three B: Nurse Redheart and Doctor Stable.

Answer three C: Mayor Mare and Filthy Rich.

Answer Three D:Coco Pommel who has caught the unwanted attention of Dr. Caballeron