Here are all secrets in the new version 0.49 of the game: The Genesis Order.
Note: If you are the old version, you can check out this guide (V0.53, V0.51) to get their corresponding secrets.
v0.49 All Secrets (Credit to rainwake)
Story
Boulder behind the Church – Drops Antique Key. Needed to open the chest that blocks your way upstairs in the church 
Church right side upstairs – Use antique key to loot the chest. You get an Old Book. Sneak past guard to progress.
Chest Key
Church 2nd floor – Need Cheese from the Farm and a container to capture Rat. please check out the V0.47 secrets guide above to find the cheese (check the Weed Killer section)
Church backyard – Need Weedkiller to clear the weed. Then the Rat to feed the cat. The cat drops the key
Chest
Andrea’s House – Piano code is C, E, D. You have to progress the story first and see Andrea use the piano before the game lets you input the code.
Chloe’s Profile
Heather’s House – Chloe’s room
Mace Parts
Forest – Go Right and check the boulder. You will find the Mace Grip
Forest – Go Left and clear the weed to find Mace Handle
Related Posts:
- The Genesis Order: All Secrets Guide (V0.57)
- The Genesis Order: V0.69 All Secrets Walkthrough
- The Genesis Order: V0.75 All Secrets Walkthrough
- The Genesis Order: V0.94 All Secrets Walkthrough
- The Genesis Order: V0.77 All Secrets Walkthrough