Beware of spoilers (doh)!
All steps can be done in any order, with exception to step 1,2 and 7 (to do step 2 you need to do step 1 first, to get true ending you need to do steps 1-6 before defeating the boss). Feel free to do steps 1-6 how you like (step 6 is the hardest one imo).

Location: Cathedral Entrace
She can be find at Cathedral rooftop:
Climb the vines, and pay 1000 to enter her room.
After answering from whom do you want to take time, choose her twice:
After second answer you will have to defeat her. Parry her attacks to get sweet counter. Dodge her scythe. After winning, she will hand over 10 meteor dust. She will also drop key card (should be in a middle of the room):

Location: Crater tower interior
The key card is required to gain access to secured room found in Crater tower interior (it's the last area before final boss).
Go to the first elevator. Fight your way through second floor. On the third floor, after getting out of a lift, go right, up, left, up, left. You should stand in front of closed doors:
Use a key card there and enter newly opened area. Go right, next to the area with M's scythe,
go to the furthest right wall:
There should be a hidden passage to a room with the blueprint (in the screenshot I have already collected it):
Blueprit obtained, you only need 4 parts now.

Location: Aquarium
Teleport to aquarium, take an elevator. Go one room down, one room right.
Stand on a platform, follow right using ice grenade or double hookshoot.
There is a hidden passage on a platform:
Fight your way through the room to obtain the item.

Location: Garden East
Teleport to statue ruins. Go down to the Garden East. Head to the left entrace through the water.
Locate 2 platforms that you had to get energy orb from:
Go left using hookshot or ice grenade to cross the water. There is a hidden path between trees top left. Go up to enter new zone.
Chest is at the top of new location.

Location: Factory
Teleport to factory entrance. Go to the upper room, move to the room to the right. Cross the lava, defeat hostile bots.
Move to bottom area (mech crate push upgrade), stand in the right bottom corner:
Use hookshot or ice granade to acces platform across the lava. After that using ice granade access platform with a chest in the bottom left most corner on this room:
Go left through the hidden passage to enter a new zone:
Chest with clock hands is at the bottom of this room:

Location: Crypt/Catacombs
The way through Crypt will be placed in other guide (I guess). To get the pendulum you will have to defeat crypt boss (which is a recolor of aquarium crab mini boss with ton more health).
It's located here:
Basically parry his claws to deal decent damage, after 3rd 2x hit boss will start spewing bullets everywhere and spawn 2 mobs (harder versions of standard enemies). Good start is to stand on his upper right/left side where bullets don't reach, and where you can parry enemies with ease.
Go to the upper room to locate chest with pendulum:

You have to make an Ancient clock by using any Crafting Table.
After obtaining it, go to the Hidden Gallery part of a crypt, upper left alkove, and place a newly crafted clock there:
This will unlock new area called -?-. Go through the platform section to reach the portal of time:
After you click yes, you will be transported to day 1 of your journey, back in the gear village.
The secret ending boss is basically the end boss with additional 3rd stage.
Get to the Crater Depths to fight the final boss, with additional stage. It's a little bit harder, but very similar to stage 2 (he has more hp, faster attacks, more dead zones, wider grab attacks). What helped me a lot was a reward from Olga (portable crafting bench) and a lot of defence,syringe, attack and stamina cogs. You should have a lot of materials at this point. Also auto syringe chip is good to have to refill your estus. After you beat the boss, grab your waifu and togeter run away from crater.
You should get the achievement :)

Hope somebody finds these guides helpful,
Peace,
Kucyk