While you have been busy getting yourself cured of Corprus Disease, Caius Cosades hasn't been idle. He has been recalled to Cyrodil by the Blades. He has also been trying to track down the Lost Prophecies and thinks that the Dissident Priests may have a copy. So before leaving the scene, never to return, he sends you after Mehra Milo, his link to the Dissident Priests. He tells you that if there is a problem, you should look for a note to with the word "amaya" in Merha's quarters.
When you get there, Merha is nowhere to be found in the Library. Ooops! It looks like there may be a problem. A short search in the Hall of Wisdom will turn up the door to Mehra's quarters, locked tight. Now Caius and I know that you'd never let a little thing like a locked door stand in the way of accomplishing a mission, so whip out the lockpicks and go to it. Be careful of the Ordinators that like to wander the hallways. They don't take kindly to trespassers, so have a few golds handy to pay the fine in case you're caught in the act.
Merha's quarters are empty, but there's a note on the dresser (along with a couple of Levitate potions) telling Amaya to come visit her at the Ministry of Truth, to talk to the outside guard about locating her and not to forget the two Divine Intervention scrolls she borrowed. The Ministry of Truth is that BIG rock floating on the eastern side of the Temple.
So up you go. The guard is on the south side of the rock. Tell her that you're visiting someone. She will be very cooperative, give you a key to the outside doors and say that she will cover for you. She tells you that Merha is in the prison cells in the cell on the far right, but says you'll have to go searching for keys. She also cautions you against fighting any Ordinators inside.
Let me emphasize that this is not the place to indulge any homicidal urges. Ordinators are very tough fighters and you'll typically find them close together, which means they will gang up on you. This will not help your reputation with the Temple, the Ordinators, or with anyone. "Sneaky" is the ticket to success. "Belligerent" will just cause trouble that you may not be able to fix.
The quickest and easiest route is to use the back (north) door. At the first intersection go either right or left (they will both loop around to the same place) and you'll find yourself at the door to the Prison Keep. If your lockpicking skills are absolutely abysmal and you don't have any "Open" spells or scrolls, you'll need to hunt around for keys. This is very difficult as there are Ordinators everywhere and when they tell you to get out, they mean it.
If you are wearing Ordinator armor (helm, cuirass and both pauldrons), you might be able to get by the outer guards. If you have risen to the rank of Patriarch in the Temple, they will grumble about it being very irregular, but will tell you where the key is. Under any other conditions, you will get one warning to get out. If you do not step out sharply or if you pursue dialogue, then they go to attack mode.
The Grand Inquisitor has an interior key on his person (you'll either have to fight or pickpocket him) and in his desk. Once you are into the Prison section, you'll need a cell key. There is one in the desk on your left. However, there are a lot of NPCs wandering in the area, so getting it by stealth is going to be tricky.
The first NPC that you encounter will be Duldrar Saren. If you are the Patriarch of the Temple, he will just tell you where the keys are. If you are higher than Adept, he will not only tell you where the keys are, he will also take all of the guards out of attack mode. If you don't meet the Temple rank requirements, don't even bother. Just sneak by him. A good Chameleon or Invisibility spell wouldn't go wrong at this point.
Work your way down the ramps to the cell on the right and open the door (key, spell or lockpick -- any will do the job). I hope you remembered to bring the Divine Intervention scrolls that Mehra wanted. One of them is her escape route. If you didn't bring it, she'll send you out to get one (and probably have a very low opinion of your intelligence since she told you to bring two).
If you have at least one Divine Intervention scroll in your inventory, she will take one and lay out the rest of the escape plan: get out of the Prison by whatever means you have at your disposal. The talk to Blatta Hateria on the docks at Ebonheart and say that you want to go fishing. You will be taken (for a modest fee, of course) to the monastery at Holamayan where she will meet you.
She tells you to talk to monk on the dock at Holamayan for instructions on how to get into the monastery, but I'll save you the trouble. The door is accessible only between 6 and 8 in the morning and 6 and 8 in the evening (the hours when Azura's star is up). Remember that -- it's the key to another door you will be encountering soon. Follow her instructions.
Once you are in the monastery, go right and you'll find Gilvas Barelo and Merha Milo in the library. Follow all of the conversation threads that you can with Barelo (especially the "lost prophecies") and you'll get three books (pieces of parchment, actually) added to your inventory. You will need to take these to the Urshilaku Wise Woman, so don't lose them or sell them. These three pieces of paper were the reason for your coming here, so once you have them and have finished talking, you can head on out.
If it's not during the time when the outer door is accessible, you're going to have to wait. There isn't much else to do here besides sleep, read and make donations to the shrines (it's a monastery, you know), so try to keep yourself constructively occupied until you can leave and report back to Cosades.