Ok, don't sue me, just saying how I'd implement it if this was mine. Agreement is not compulsory.
The idea is that when the titans were banished, one titan in particular (to be named) tried to avoid banishment by binding himself to a shard. For the most part, this did not succeed - the titan was banished, but he had succeeded in some small measure. The titan's will, his ambition, his purpose, had become imprisoned within the shard. So the will of the titan can't escape the shard, and while the world slowly starts to rebuild, the titan's will grows mad, and eventually corrupts the shard (bends it to his will) while trying (and failing) to escape.
Cases:
- Body banished, no mind. The mind "attached" to the magic flow of the Shard.
- Body dead for all purposes unless the other Titans in their pocket universe are fond of keeping vegetal bodies alive. Considering what we know of the Titans, I vote for dead body. The original mind is in the flow of the Shard, having lose (most if not all) part of its own power and getting the ability to manipulate the flow of the Shard (affecting the power that can be obtained from it).
- Like the previous point but we keep the body alive. Why? The Titans know what happened to the Titan and keep the body to try to use it as a way to come back to Elemental or something like that. This option is only interesting if it can be developed through the game (quests, events...).
- Body banished, mind intact in it. Copy of the mind "attached" to the magic flow of the Shard.
- The Titan does whatever Titans do in their world. The mind in the Shard is like previous case with the difference that it may be conscious of being a "clone" or not.
- Body destroyed. The mind (copy or not) "attached" to the magic flow of the Shard.
- The mind in the shard may know or not about the destruction of the body and/or about if it's a clone. In any case, works like in the first case.
In any case, considering how long lived Titans are, maybe it doesn't go mad per se (frustrated on the other hand...). In any case, his objectives would fall in the line of: get a body (real or manifestation?) and control the power of the Shards. You can twist those objectives and/or the way of obtaining them but I'd say that those would be the most expected objectives for him to achieve. Ok, maybe world destruction if he goes totally nuts. 
At this point, species X comes along. They have, of course, heard stories about channelers bringing the power of the shards to work for them and recreate civilization. Eagerly, they make the necessary preparations, but as their fledgling channeler tries to tap into the shard, the titan's will is found instead. The titan's will then convinces the species X that he will teach them all the wonders of the old times - specifically engineering (that was the titan's speciality). The titan's will uses the magic within the shard to bring power to a basic technological society. The titan's will tells species X that they can become more powerful than anybody else, if they combine this engineering with his power to control all the shards in the world.
Being trapped for so long in a Shard and being (what is left of) a Titan, it would be possible that when the Sovereign tries to tap into that Shard... Well, bye bye Sovereign. Hello Titan. It does not need to happen instantly (especially because it would be the first time that a Channeler tries to use his Shard) but could slowly happen (in gameplay terms, it could actually happen to anny of the Channelers of that faction). After all, Channeler do channel the magic flow from the Shards so in this case, it would be like inviting the Titan to enter their bodies (temporarily though). It may not take possesion of the Channelers, but I'd say that it would have at least some corrupting effect the more they enter in contact with the "tainted" flow from the Titan Shard.
The goal of the titan's will remains the same - to conquer all and harvest the shards for himself. The species sees the power of the shard used for a measure of good, in the beginning. They believe that the titan's will can help them create a better world, perhaps not even just for themselves but for everyone.
Yep, yep. Don't forget the body. Shards are attached to the world so unless there is some kind of "magic plane" he can dwell in, he surely would want to walk free over Elemental.
The gimmick of the species will be engineering and chaos (randomness). Their spells are as likely to work for them as it is against them. The idea is to have abilities that can blow up in their faces, or just generally do random things to everyone. I haven't decided on the source of this randomness - either it is because the titan's will is now mad, or it is because the will of a titan lacks the real power of a titan and thus the power he lends to his subjects is not really within his control. New shards will be corrupted by the titan's will to feed the society growing. As the society grows more powerful, the dangers of the randomness will go up (but also their powers). Perhaps the titan's will has problems managing all the power, or perhaps he just likes to see his minions bleed.
I designed a magic (theoretical) system (for Elemental) based on some randomness. The idea in my case was that magic was very powerful but the magic users were the first ones so there were no tutors or books to learn the tricks. Which meant many magic users exploding or worse.
For your case I would go for the Titan's will being able to control the flow from the Shards under his influence. That would allow the faction to actually wield more powerful magics than other factions. Problem is: they are still the same people with "advanced magical weaponry". Each spell learn by the faction is more powerful than the average but has a chance of backfire. The more powerful the spell, the bigger the chance of backfire.
As example, lets suppose a Teleport. As a "basic" spell, it would work normally but with a very small chance of backfiring (in this case, it would cost mana and you wouldn't teleport). Later a new and improved version of Teleport is discovered (lets say that it allows you to Teleport anywhere except in enemy territory) but it also comes with an higher chance of backfire (in this case, the army ends in a random tile). Later again, another improved version of Teleport is developed (allows you to teleport anywhere) with an even higher chance of backfire (lose the army, including Sovereign if in it).
Obviously, magic users of the faction would research techniques to reduce risks of backfire (meaning that they start learning to control the increased power that the Titan grants) but the most powerful spells would always have some risk.
I mention this because altough it has randomness built in, it feels better than just randomness. But it's just an idea trying to... er... validate why would the faction have problems controlling their magic.
Eventually, if enough shards are corrupted, the titan's will can attempt to summon his body and power back to the world. As that would be at the very high end of the power spectrum, it would have a very low success rate, and would more often summon various hostile monsters that would go rampage across the empire. However, it should be possible to summon the body back. Some alternate mechanic would be in place here, like allowing the user to control him two turns, then four turns of madness.
Summmoning a new body (or the old one) or taking control of the poor Sovereign (or a poor Channeler Champion). I don't think it's bad to get a Titan controllable the same as you can get a Dragon. It could affect negtively the magic performance as the wouldn't be part of the Shard... or maybe not, depending on the effects of being free from the Shard (and how selfish he is, my precious...) and which ties remains.
