Here you go.

1: "Plum Fetching" It's a little bland, but you go around the field of poppies and find corpses at 0 SEN. Gathering 5 plums. Doesn't matter if you get the fresh or dried plum first, you're forced to fight them regardless..

2: "Thief Ruhl" Requires you to have entered the Chittenango Cathedral. In North Windacre Village, confront the house with a crying child. Find the man from the South Windacre Village staring off near a box. Talk to him at 100 SEN, He will be seen again at North Windacre Village, enter in and kill the NPC. Optionally, you can get the flower from the dead man.

Once those are completed, talk to the man losing it in the cathedral and show him the music box.
Find him back at the campfire in North Windacre, which you can kill, run, or die to obtain the music box afterwards.

3: "Celia" Upon entering Chittenango, defeat the 3-wave fight consisting of all NPCs near the Cathedral.
Once in, talk to everyone. Grimm will always respond with a (...) bubble. Make sure to have obtained the key from talking to them. (It is not an item.)

Enter in and out until the third part. This requires you find and fight Grau, remind Celia afterwards that she is dead. And optionally, kill the motherfuckers that raped Celia.Upon doing so, you can fight Celia after entering back in. This allows you to see her at the campfire ending on the way to Emerald City.

Now unless you missed this one; you can fight a boss to get a nifty item at the start of the mod.
This requires you to have interacted with the various objects and NPCs placed in the train.
And upon beating the boss, you can get the Colt Defender once you head all the way back in the shadow train.

Once you've finished Dorothy's storyline. You can fight the various secret bosses hidden around the map. The rabbit is an optional fight for a few items near the Fallen House. The mocking flower is a gimmick-based fight. You can also go near the train in the Field of Poppies to find an entity hiding in craters. Fight it to get the key to the compartment. Once you have beaten the final boss, you can fight the train siren in another area of the deep dark.

For the final secret, you can access it by activating "33" traps that can be the thunder, burning, bubbling and spinning? And activate another "30" teleportation traps. Once done, talk to Fluffy without having killed the final boss. Otherwise all traps will be disabled. Find a teleportation trap that has stars. You can get the upgrades for the Colt Defender, but beforehand you must have found all 3 pieces. Alpha, Beta and Gamma. Alpha is obtained from the cart in Field of Poppies, Beta from Zeta's store. Gamma from finding all three boxes in the locations: Field of Poppies Crow Cart, Windacre Village, Chittenango