You must rescue Agrippa and obtain his head. To save Agrippa, you must make the Weyer's Tonic.
For the Weyer's Tonic, you need Vitae, a poisonous mushroom and Tampter. I highly recommend doing all of the gathering BEFORE gathering all six pieces of the orb and entering the Chancel.
GATHERING THE INGREDIENTS
Tampter is obtained by grabbing the Hunk of Meat (in the room with all the cells before going to the Chancel, it'll be upstairs) and lowering it into the well (near the Transept). The invisible water monster you encountered earlier will eat the meat, and once you pull the string back up, you're left with a bone with a bit of Tampter on it.
The vitae can be gathered from a room in the Transept. Go into the room with the sawing torture device and look on the ground for a grate. Open the grate and you will see the blood inside. You must combine the Glass Jar with a piece of string (the piece of string can be found in Alexander's study - on top of the spiral staircase in the Transept) and lower this glass jar into the blood to gather it.
The poisonous mushroom can be found in the Choir. You should see a large mushroom cap on the ground near the door entering the torture room with the Brass Bull. Use your hammer/chisel out of the inventory on the large mushroom to gather it.
MAKING THE TONIC
You cannot make the tonic until you've entered the Chancel with all six orb pieces. After Daniel is captured, he can make his escape and return to the Nave. Parts of the Nave, the Transept and the Choir will be destroyed. This now gives you access to the laboratory. With all ingredients, Daniel can now make the tonic. Once the tonic is completed, use it on Agrippa to "free" him. DO NOT FORGET TO BRING AGRIPPA'S HEAD WITH YOU. Using the tonic is not enough. Daniel must find a hand saw and use it to chop off Agrippa's head.
SAVING AGRIPPA
With Agrippa's head in tow, enter the Inner Sanctum and confront Alexander. Patiently wait around long enough for the portal to open (basically stand around and do nothing for a few minutes). Take Agrippa's head out of the inventory and use it on the portal. This sends Agrippa through the portal, and the achievement will pop.