i like it!!! good work!

Firstly do not give alternate sequences unless you're doing a choose-your-own-adventure story. It's not serving the plot differently because you're only writing one story and not two versions. As the author you need to decide which sequence you are going to use, or ask beforehand. In addition no one wants to read the whole chapter and then go back to the beginning to see a possible difference that won't affect what they just read.
I might as well ask how Shadow suddenly has money to buy stuff. Considering he woke up in the middle of nowhere and didn't have a clue about anything.
And how come he isn't thinking more about what happened to him. He remembers he was a human and now he's a mew and just decided to start a rescue team without even thinking about it.
Since you said that * is for an area with two possible text versions why do you have sigh between two *'s? This isn't an rp where you just put actions in little marks, they can be expanded on. It makes the story better to read.
It's pretty odd he's already thinking about love when he doesn't even know anything about Spark.
Not much happened in this chapter either, except confirming my earlier thought that this just seems to be some sort of copy of Mystery Dungeon, which doesn't bode particularly well.

Shadow's thoughts for spark in this chapter originate around the fact he had a strong bond with his old Raichu, Sparky. Most of what he saw in Sparky, who was a Female, he now sees in Spark, another male. The money was that which was in Spark's possession, not Shadow's.
Also, as they just began, only Spark really fully knows about his abilities. If you played the game, the first mission is from buitterfree, to save her son, caterpie. If you want to know more there, buy, and beat, the game like i have.

I beat the game ages ago, that doesn't mean I remember every little detail. And why are you copying the game so closely?

Have you ever read a few of the other PMD fanfics on AGNPH?
You HAVE to start out, for the beginning at least, following the procession of the story, while slowly twisting and warping the plot to fit your storyline. Thats how they always begin. Trust me...the rescue theme will stay in place, but things will get much more involved. (warning: PMD Plot spoiler ahead) Also, the story will include the meeting of an Absol, a growlithe, a vulpix...Rayquaza, Jarachi....even Celebi. Though their roles, I may say, some differ from that in the game, and some are added.

Have I mentioned...This story also will contain: Death, gore, violence, depression...as well as M/F, and M/M/M/F?
This IS only the beginning. Stay tuned....this is only a glimpse at what my style includes.