use the first cipherplate on a box with wires connected to (in place 5-5-2), put it in the second hole. Go down and left

Click the wheel on the pipe.
Continue to click on the wheels.
After the title screen...click the pencil and paper on the floor. This gives you access to notes.
Go left. Open the hatch on the floor by clicking the levers at the sides, then the central mechanism. Go down and down.
Go left. Click the button on the computer under the table. Read the three panels on the computer screen.
Go right twice. Click the button to open the door to the Portal. Step inside.
Go right and open the hatch. Go down twice, then right.
Enter 5-5-2 on the Portal machine and click the button.
Welcome to the Root! Click to the left of the machine and follow the route down to the Secret (1/5). Go back.
Follow the metal walkway to the right until you see the crack in the wall. Enter it and go right.
There is a brown Lead Casing item here in the middle of the screen. Pick it up. Continue right.
In the room with the power box there is a fallen pillar with a plug attached to it.
Click the cover on the power box to remove it.
Click the latches on each side of the plug (look carefully). Click the plug twice to switch on the power.
Go right and down.
Go right three times, then take the ladder up.
Open the grey box by clicking on it. (not sure what this does)
Go left twice. Enter the room. Pick up the Wrench on the floor, under the chair.
Leave the room. Return to the floor below, to the room with a ladder through the floor. Go down.
Go right. Use the Wrench to remove the bolts on the grey panel.
Take the Rusty Key. Go up two floors to the room with the empty boxes on the wall. Enter.
Use the key on the leftmost box. Take Cipher Plate 1.
Go down to the floor below, to the room with the grey box with a button and wires coming from it.
Put the Cipher Plate 1 in the slot on the RIGHT of the transporter, then click the button.
You've arrived in room (0,1). You can leave the Cipher Plate 1 in the box for now. Go down and left.
Pick up Cipher Plate 2 on the chair.
Go right and down to the bottom.
Go left. Use the Wrench on the panel. Collect the Secret (2/5).
Go right twice. This is the charger room. You'll need to return here later. Go back to the transporter (up the ladders).

STAGE 2
You need to understand how the transporter works. There are two Cipher Plates and two slots on the transporter, Left and Right. Putting Cipher Plate 1 in the Left slot and Cipher Plate 2 in the Right slot will send you to room (1,2). So there are 7 possible destinations. The Root area is (0,0). Got it? On we go!
Go to room (2,0). (That's plate 2 in the left slot, nothing in the right slot.)
Click the hatch to open it. Go down. Click the top button. The needle should point to the right. Go back up.
Go left and repeat. Pick up the Empty Coil inside the hatch.
Go left again and repeat. Go left and take a look at the brick wall. Return to the transporter. We'll return here later...
Go to (0,1). Go to the charger. Put the Empty Coil on the raised platform on the charger and click the handle on the wheel three times. Pick up the charged Coil.
Go to (0,0). Go right twice and put the coil into the slot.
Go to (2,0). Go left twice. Click the button to open the box for Secret (3/5).
Go to (0,0) and get the Coil.
Go to (1,0). Go down and right. Put the Coil in the slot.
Go to (0,2). Go down and left. Green symbols are visible on the displays. Go all the way to the left.
Click the wheel. You should hear something being released. (If not, maybe the coil has to be in (0,0). Haven't checked.)
Go to (0,2). In the room all the way to the left (where the wheel on the pipe is), click on the part of the floor behind and to the left of the pipe for Secret (4/5).
Go to (2,0). Go all the way left past the brick wall.
Take Wisdom Gem 2. Go left and up the stairs. On the chair is Secret (5/5).
Go to (1,2). There are four rooms here, arranged in a circle around a fifth room.
Click as follows: into the room, right. Click the light bulb by the door to take it.
Go through the door. Go into the central room.
There are three holes in the wall at head height. Look inside them. You'll see a metal mechanism. It looks like a clock.
You have to line up the "hand" with the ornate thing on the side/bottom/top of the "clock face". You can do this by going through the rooms and clicking the wheels. It's not that difficult...Go on...
When everything lines up, you'll find a Metal Box in the central room. Take it.
Go to (1,0). Go down and right twice. There's a tiled tub here. Click the little brown label on the right to get a note.
Click the top/inside of the tub. Drop the Metal Box into the tub and watch it dissolve. Go back.
Use the Wrench on the outflow pipe on the right of the tub.
Take the Wisdom Gem 1 from the tub.
Go to (2,1). Go right and up.
There are two switches here, one on either side. To open the gate, make sure both have a white light on the RIGHT.
Follow the room onwards. Use the light bulb on the holder in the dark area.
Go left twice. Check your notes for the symbols you saw earlier in (0,2). Click the corresponding ones on the wall and then click the button underneath.
The ladder should slide down. Go down.
Use the Lead Casing on the top slab of rock.
Remove the Lead Casing, then use it on the two other slabs.
Go down and get Wisdom Gem 3.
Return to the transporter (you need to change the switches to get past the door again).
Go to (0,0). Go back to the Portal machine.
Go to 7-4-7. Go right twice. Open the door and go right.
Place the three Wisdom Gems in the diamond slots on the wall.
Click the handle on the control panel to the right.
Congratulations, you win! (With all 5/5 Secrets!)

you should be in "The root" and find a metal box with a button on it that doesnt do anything, put the cipher in one of the slots and push the button!

where you press the button on the box to open it

I push the button but it just sits there and doesn't turn white. :*(

the slots are located at the top of the box... there are two slots (rivet, slot, rivet, slot, rivet).

where's the lead casing I'm supposed to use on the three rocks??

there WILL be a submachine 6!