Nepenthe is largely linear overall in nature, but choices you make at certain events will cause the ending and rest of the game to unfold differently. Below is a screenshot of The Ruins, specifically an area that matters the most for the differences.

The buildings are as follows:

• Red: old man NPC w/ lore and advice.
  
• White: House, contains teddy bear on left and ROPE on the right.
  
• Green: Cemetary. Not a place you can enter.
  
• Grey: Doors require a PICKAXE.
  
• Blue: Doors are LOCKED and need a key.

In addition, the Small Town to the left of The Ruins has important buildings to enter.

• Far left is Porkchop's house. Location of PICKAXE-related choices.
  
• Grey/brown left house is the Werewolf house.
  
• Tan/brown house (potentially) isn't necessary.
  
• White/blue house on the right is the Shopkeeper's place. KEY-related choices are here.

Getting either PICKAXE or KEY will lock you out of the opposite's paths; acquiring the Key from the Shopkeeper causes Porkchops to leave, and dealing with Porkchops causes the Shopkeeper to refuse talking to you.

Everything else is linear or up to you to explore and sidequest through. The Endings will reference these two above locations multiple times, so refer to them as needed.

ENDING 1 - Worst

Play the game as normal until you have the option to rescue the old lady from the pit in The Ruins. DO NOT rescue the old lady, and continue on either KEY or PICKAXE routes.

If on the KEY route, attacking the ????? in the Underground area might also be a trigger for this ending if you DID rescue the old lady.

Regardless, route ends in the Magistrate's Castle with forced fights followed by an escape sequence. Touching any of the advancing ninja guards results in an instant Game Over, so avoid and escape down through the gate previously blocked by a bat NPC in the Castle town.

Play the game as normal until you have the option to rescue the old lady from the pit in The Ruins. RESCUE her (the rope is in the white-outline building on the Ruins screenshot).

If going down the KEY route, make sure not to attack ?????? in the Underground.

If going on PICK AXE route, do NOT talk to Mograth on the far left side of the Small Town next to the Ruins, and help out Porkchops before you take the Pick Axe from him.

Game should then run the full length up to meeting Hado Ream, and leaving his house for the ending sequence.

Play the game as normal until you have the option to rescue the old lady from the pit in The Ruins. RESCUE her (the rope is in the white-outline building on the Ruins screenshot).

If you visit the old man in his house in the Ruins, his CAPITALS speech will give you the hints necessary for this best ending.

Do NOT get the Key at all from the Shopkeeper.

Do NOT help Porkchops at all (easiest to directly steal his Pick Axe and fight him).

MAKE SURE to go talk to Mograth at the far left side of the Small Town and show him the Note.

Continue through the Ruins, the Underground, the Magistrate's Castle, and to Hado Ream.

Regardless of the outcome of the final battle (kill/spare), you should trigger the best ending and the neat credits sequence.

• If you talk to the Shopkeeper in his Secret Store, you can buy Baked Potatoes for 0 Gold and then sell them back at a profit. A full stack of 99 will give you just over 7000 gold, so exploiting this to get whatever items you want are handy.
  
• Many enemies (as of 6/16/18) can be dealt with multiple ways. Try Relaxing multiple times to see what happens, or using items on enemies. Some enemies require being defeated using Attack, though.
  
• You can skip the tutorial fight with the Trainer, but going through the motions of it and finishing it will net you experience no matter what. If the Trainer is your first fight, that will level you up, making successive fights slightly easier.

I want to thank @IndieGamerChick and the game's developer for doing their giveaway of this for #IndieSelectE3 on 6/15 - 6/16. Was really fun to replay this multiple times to figure things out, and I plan on doing an Achievement guide once the dev has them working.

If there's any errors or additional information needed to further help or clarify this guide, please comment, and thanks for reading!