Now to Thomas.
We don’t know what deal Nemesis; or its proxy HWWB, had going with Lord Raith. We don’t know if Lord Raith was nemfected or if he was just a useful idiot who thought he made a great deal to get immunity from most forms of magic, but didn’t realize he would be helping Nemesis end the world as he knew it. Which version of Lord Raith is true may might be important or largely irrelevant. (Personally, I think Lord Raith falls into the useful idiot category or at least the WAG I'm about to spin works better if that is the case.) What I think matters most is Lord Raith wasn’t given his magical immunity without the expectation there would be a major payoff for Nemesis and its Outsider minions somewhere down the road.
The problem for Nemesis started when Margaret LeFay’s death curse neutered Lord Raith. Whatever big things Nemesis expected Lord Raith to do or contribute to couldn’t happen because Papa Raith was forced to play safe to conserve his remaining tank of energy. This would have been especially perplexing for Nemesis if Lord Raith wasn’t nemefected, because I seriously doubt the White King would have shared the knowledge of what Maggie Sr. had done to him with HWWB. Whatever the case may be, Lord Raith’s value to Nemesis would have plummeted. A backup plan was needed; if Lord Raith wouldn’t or couldn’t deliver the goods Nemesis had to find someone who might be better suited for the task.
So now you might legitimately ask why Nemesis wouldn’t target Lara Raith to be its new tool and Papa Raith’s possible successor. Thomas gave us the answer to that in Blood Rites when he told Harry, "Lara is one of the most capable, intelligent people I've ever met. But around him (Lord Raith), she turns into an obedient dog.” Nemesis needed someone who could be seen as a legitimate leader of House Raith and the White Court, by the rest of the White Court. Nemesis might not understand human or White Court vampire family dynamics, but I think it would calculate that someone who acts as Thomas described wouldn’t be a good choice. On the other hand, Nemesis would understand that Thomas kept surviving Lord Raith’s attempts to kill him. None of Papa Raith’s previous sons had shown such survival traits. So, Nemesis chose Thomas over Lara. Oops!
So now you might want to know when Nemesis got its hooks into Thomas and why I have said Thomas might be a sleeper agent; or more accurately, have a sleeper agent implanted in him. Remember the conversation Cowl and Kumori had with Harry outside of Bock Ordered Books in Dead Beat? Specifically, look at what Cowl said to Harry after Harry told the necromancers he recognized them from Bianca’s party where they had acted as her flunkies. First Harry said, "That was such an amazingly screwed-up evening. It's been coming back to haunt me for years," To which Cowl replied, "And will for years to come. A great many things of significance happened that night. Most of which you are not yet aware."
Many things? I can’t put a number to the word many, but I believe it must mean more than two things occurred that Harry didn’t know about, and for the longest time I could only think of two things that Harry wouldn’t have known about. First, Harry didn’t know that the Athame Lea had been given had been tainted by Nemesis. Of course, Harry didn’t even know about Nemesis then. The second thing Harry didn’t know about is only conjecture, but it seems likely to me that Mr. Ferro’s gift; the box with something that glittered, was also contaminated. The thing is Thomas received a gift from Bianca too. Yes, I know it was just an envelope with a deed for a condo in Hawaii and a single plane ticket. Lea was given a magical item; however, there’s no way of knowing if Nemesis needs to be transmitted through a magical item. The gift Mr. Ferro was given appeared to be cask with diamonds or other gemstones in it. There is no reason to think they had any magical properties other than Nemesis contamination. Harry didn't physically touch his gift.
Now consider what happened after Harry and Michael escaped from Bianca’s party. Thomas got away as well, but he also managed to snag Amorachius in the bargain. How convenient. Thomas foils another of his father’s plans to get him killed and makes a new friend, and soon to be ally, who is also a powerful wizard of the White Council. A wizard that Nemesis; or at least one of his top lieutenants (HWWB), has an interest in. Harry had foiled two Nemesis plots in just a few months the prior year. That might not have been enough for Nemesis to see Harry as a major threat, but it was certainly enough to draw its interest. So, I’m suggesting Thomas was allowed to pick up Amorachius, knowing where he would take it. Also, remember that I’m suggesting that nemfecting Thomas is just a backup plan for Nemesis. If Thomas had allowed himself to be killed by Bianca’s first wave of minions, he wasn’t qualified to be the tool Nemesis might make use of in the future. Plus, from Nemesis’ perspective, there is still the possibility Lord Raith might come through for them. I think Nemesis would only discover this wouldn’t happen after the war between the Red Court and the White Council started and Lord Raith and the White Court remained on the sidelines.
After the events in Grave Peril the implanted personality sits and waits for an opportunity to move against Lord Raith but no opportunity arises. Remember, if Lord Raith is in the useful idiot category, that means Nemesis most likely doesn’t know about his weakness. It can’t risk pushing Thomas to make a move that will almost certainly fail. During the events of Blood Rites HWWB; and by extension Nemesis, might have finally learned why Lord Raith wasn’t holding up his end of the bargain. If it also realized that the White King might be able to recover his mojo by killing Harry and Thomas, that would have been welcomed by it. Remember that Thomas was only a backup plan. If Harry and Thomas defeated Lord Raith, then the hidden personality could be activated. Unfortunately for Nemesis, Harry screwed up its plans by getting Lara Raith involved. Nemesis never saw that coming.
There’s one huge objection I know many of you are going to make. Harry and Thomas shared a soulgaze. Seeing the Nemesis infection should have floored Harry. I don’t think so. Think about this, Thomas never said anything like this to Harry: “Harry, when we shared that soulgaze, not only did I see things about you, I also saw this beautiful woman standing next to you.” Remember the crazy stuff Harry saw when he shared a soulgaze with the bearer of Ursial’s coin? Lash was already inside Harry’s head, but she was only speaking to his subconscious then. That’s why Thomas wouldn’t have detected anything out of the ordinary. If Thomas wasn’t taken over by the Nemesis personality, if it was remaining dormant until some trigger event activated it, it may have been largely undetectable.
I almost forgot. Even if a nemesis personality is hiding in the background of Thomas’ head, by now it might be having an effect on Thomas anyway even if it's not giving him specific orders. Nemfection allows a magical being to change its true nature. Whose nature has changed more than Thomas' has, other than Aurora's and Maeve's did?
P.S. If I'm right does that mean that Thomas is doomed? Maybe not. I think that even as strong as Thomas is compared to normal mortals, I doubt he could survive being stuck inside a big ball of ice like Lea was placed in by Mab. However, even though I've stated that Lilly was an unreliable narrator when it came to knowing what Nemesis is and how it works, her description of Nemesis infection as a spiritual malady suggests to me a possible cure for Thomas, though a long-shot one. Lea had just enough presence of mind and inner strength to go to Mab to seek help after she realized what had happened to her. If Thomas has that same inner strength and if he could go to Harry before he was completely overcome; and I mean go specifically wherever Harry's new digs are going to be, the Sword of Faith will be there too. If anything could banish a spiritual infection, I think taking up Fidelacchius might do the trick.