Appendices: Starter Quests
This is a guide to any starter that you can't just catch or easily find in the wild.
Squirtle
First, follow the guide in Chapter 9 to unlock the PULSE Garbodor grotto. Inside the grotto, there's a hidden door behind the left reactor tube; keep walking to the right (ignore the strength rock) until you're outside again. There's some non-euclidean geometry here; first, slide down the path and enter the cave. Climb the ladder once, then go back down the ladder to enter a different chamber. Push the strength rock downwards, jump off the ledge, and push the second strength rock to the left to open up the path to the north.
You'll find the Squirtle relaxing in a wastewater pool, and TM12 Taunt directly below.
Chikorita
If you didn't already, catch a Chimecho (via Chingling) from the cavern underneath North Obsidian's stairs; then, head to Azurine Island once again. Make your way to the former Meteor building and show the guy hanging out there your Chimecho. If you go into the back room, you will find a Chikorita!
Cyndaquil
When you buy all of the Pokémon in 7th Street, Cyndaquil is one of the few that has no relevance to any later quest. You can take it as your own.
Treecko
Treecko is found as a reward for making the Devon Scope, which is required to rid Neo Beryl Ward of the invisible Kecleon everywhere.
Devon Scope Walkthrough
The obvious trap room in the first Devon Corp building had some items in it, so let's return there. The shock tiles here are now random, so enjoy being zapped all the way through. There's also a really funny troll that I have no choice but to accept and not tell you what it is.
At the top, you'll find the Devon Scope as well as TM81 X-Scissor.
If you return to Silph Co, you can talk to the attendant and give it to her and she'll give you the Silvon Scope. Armed with it, you can now interact with the invisible objects in the Jasper and Beryl wards, and defeat them to unblock your path.
Return to the jungle and jump down the hole into the Underroot.
Make your way to the bottom of the Underroot to find a pool of water; armed with Surf and Waterfall, you can make your way across it (you can also find the Blastoisinite here to the side). The only path in the new area will be blocked off by a horde of invisible Kecleon; activate it to reveal all of them. After fighting twelve Kecleon (some of which know fucking Fake Out!) you'll then have to fight the mysterious Purple Kecleon.
Finally, open the cage to find a Treecko. All the Kecleon in the wards will be gone now.
Tepig
After getting Strength, return to Pyrous Mountain where you can now push all the boulders that were sitting in the former lava pools.
You need to push the boulder into the hole. It's pretty easy to screw yourself here, so save beforehand and then follow the red arrow to push it. Jump down into the hole yourself to find... a Tepig? If you talk to it, it runs away, all the way down to B1F: now you should go and find that Strength boulder you remembered. If you push it out of the way, you'll find the Tepig again, as well as TM37 Sandstorm.
It flees once again; this time to the top of the mountain. If you interact with it again you can encounter it in a wild battle, and then catch it if so desired.