So we have 2 facts:
- The taint would go on after the darkspawn are erradicated.
- The red lyrium - normal lyrium corrupted by the taint- would still be a threat.
The answer would be to combat the taint. To discover an antidote or vaccine against it. But so far, no one knows what the taint is.
The Architect, in his own limited way, found a way to at least end the darkspawn threat by ridding them of the calling. He used Grey Warden blood to concoct a potion that can be drunk. However, they still carry the taint within their bodies, being able to infect other races.
Avernus also found a "cure" through blood (the mage you meet in Soldier's Peak).
The HoF is travelling the world seeking this cure. This might be the main theme of DA4. What is the relation between the taint and blood? From here on, we can only do guesswork. Judging by the Wardens's fate shown in the DA:I epilogue, Weisshaupt knew what the taint was all along. However, they chose to keep it a secret. If they knew what the taint was, so they knew a way to find a cure. Weisshaupt may very well have chosen to let millions of Wardens die from the taint rather than share that secret.
Because of this, we hear the Wardens have segregated themselves from Weisshaupt.
Why did Weisshaupt keep the taint a secret? And what is it?
My guess: the taint is blood magic, possibly residual blood magic from the blood sacifice the seven Chosen Magisters did by killing thousands of elves to open the Veil and enter the Fade.
And Weisshaupt knew this all along.
So why keep this a secret?
- In the DA wikia, we learn the first wardens were a group of people from Tevinter who did research to try and defeat the Archdemon. When the dragon dies, his soul travels to the nearest darkspawn, a process which makes him immortal. The Tevinters then worked to find a countermeasure. The only thing they managed to produce was to infect a man with the taint and delay the infection for 30 years.
- Shortly after the first Blight, the Chantry was created. Anything Tevinter related was deemed unholy. Any blood mages were hunted down.If the Joining is a Tevinter ritual of blood magic, the Wardens would have been banned and exiled, possibly even hunted by the Chantry.
The only answer Weisshaupt had to preserve the Order was to keep this knowledge a secret.
Proof that the taint and blood are closely related:
- The Joining is a blood ritual, although one where you don't slit your wrist.
- The Architect develops a cure based on mixing blood.
- The dark ritual made by Morrigan involves transfer of blood. She acquires the taint through sex.The taint, however, may not have affected her and traveled to her fetus.
- Fiona got rid of the taint in a sex ritual. A ritual that conceived Alistair.
Those are my guesses so far. To sum it up:
The taint is residual blood magic from the original ritual that opened the first Breach fourteeen hundred years ago.
And the reason for Weisshaupt to keep this a secret is because the cure for the taint was a Tevinter blood ritual that would attract the Chantry's attention at the time and threaten the Order's very survival.
o/