Let me preface the actual theory with my take on the nature of Fain/Mordeth/Mashadar:

There are countless ideas as to the nature of Fain, but all of them agree that he is something different. He is a manifestation of mankind, maybe our hate, as is indicated by the madness shortly before the fall of Aridhol. Mordeth was trying to fight the shadow with shadow-like tactics that ultimately resulted in a new reservoir of energy/force known as Mashadar.

I consider Mashadar a force created by mankind that can grow as long as some part of it remains. This can be seen in many scenes, most notably when Mat took the dagger, Rand destroyed Shadar Logoth, Morridin saved Rand, and other methods of dealing with Mashadar (Moiraine warding against Mashadar's tendrils). In each of these situations, parts of Mashadar are destroyed, but grow back. It is known by every Aes Sedai that taking something from Shadar Logoth is not a good idea for, in the words of Moiraine, this will let Mordith "...wreak his evil on the world again."

But how much can he grow?

We know Mashadar was initially confined to Shadar Logoth, and it seems he can only grow so much there. But when Mat escaped with the dagger, Mashadar's presence was definitely noted. It almost certainly grew at that point, and beyond all doubt when the dagger came into the possession of Fain. Ever since Fain's possession of the dagger, his powers only grew. However, there was no indication at this point that Shadar Logoth was in turn losing power.

In order for us to determine that Mashadar’s growth is limited, we have to see some shift in his power, or prevalence in the world, from one place to another.

The only time that I can find of Mashadar's growth/size behaving in this way was after Rand had destroyed Shadar Logoth. If it could be said that Fain’s power grew significantly at this time, then that probably means Mashadar growth is limited. (Shadar Logoth power down = more to go around to Fain).

I am of the opinion that Mashadar has infinite potential, and should this be the case, then my following theory has all the more weight.

Theory: Rand will seal both Padan Fain and the Dark One together, which will in turn prevent the DO from escaping and will end the cycle of Ages.

It has been thoroughly noted at this point that Fain hates the DO and would take any clear opportunity he could to deal a blow towards his previous master. We have also seen that he can completely face roll a Myrddraal with Mashadar’s power. No one knows, in this age, how they make Fades, but I’m willing to bet they involve something from the DO.

As said before, Mashadar is a manifestation of mankind’s hate. But only a manifestation of something larger, because it continues to grow given enough room. This indicates it is some force, or has become some force, similar in attributes to the DO and Creator. When Fain and the DO are sealed together, this similarity could mean they would be near equal. No doubt, some will argue that Mashadar is not powerful enough to match the DO, however, both powers would be fighting in the prison made by the Creator, which is outside the pattern. In this way, I think both powers would be able to manifest themselves fully. It is only when any of these ultimate powers of the universe attempts to enter the world when they start encountering problems.

Also, because they are almost eternal forces, and the prison itself is outside of the pattern, Mashadar probably wouldn’t be able to destroy the DO, and vice versa. But we also haven’t seen the effect that the True Power has on Mashadar, unfortunately because we don’t know the makeup of a Fade. Thus, we don’t know how effective Fain will be in fighting just the DO; pure True Power. However, the True Source has shown it is capable of effecting Mashadar, meaning that a seal of the True Source might keep both forces inside the creator’s prison.

Pair this with the fact that Fain is going deeper and deeper into the Blight, presumably to meet Rand at Shayol Ghul, and that he is basically mad, it wouldn’t be too far to say that Rand and Fain could reach an agreement that would end with Fain in the seal. The concept of fighting the DO for the rest of eternity, even if there is no winner, would seem pleasing enough to the madman. Especially since he would be pissing the DO off for literally forever, which brings me to my next point.

There are theories revolving around what powers/items Rand will use to make the new seal, but most are based on him finding some secret combination of the True power, True Source, and/or Callandor. Many of these hold some weight, but given that the DO has all of ETERNITY to work out a way around whatever seal Rand puts in place, I think he has to be preoccupied in some way.

Enter Padan Fain. With the DO fighting Fain for the rest of time, some of his power will be diverted in that effort. This in turn prevents him from having the muscle to re-bore through the new patch, and thus the battle is won.

There you go, make of it what you will.