DISCLAIMER:Any theory that is posted is just in fun. I am posting these as a reader myself, imagining I'm in your shoes and what you would think. None of these theories have potential spoilers in them and can be taken how you want to take them. They may or may not be true, but that's up to you to decide.
Samuel Royce had been exiled for nearly 5 years before returning to Cephri 6 months before the story takes place but when he returns he acts strange around others.
1.His roots in Eilleas.
2.Centros?
3.His "mission"
4.Motive
Samuel travels Eilleas immediately after his exile after The Youth Rebellion. Where he later works in the Dragon Company, for about 2 or 3 years ranking as a lieutenant when he eventually leaves. Samuel then goes to Neropos and sees the dragons of Rhaenerys. He mentions the dragons in practically a throwaway line but why? They are dragons, not seen for centuries but Samuel glosses over them. Let's analyse the lines about Neropos.
'What he saw he could not put into words. Dragons. '-Samuel I. Samuel hisself viewed the dragons with his own eyes suggesting he had close contact with the dragons, I imagine simply not just anybody could view the dragons and this line again suggests he was in close proximity with the dragons. The next line 'There were three of them all hatched in the same year together in 895 AC the same as The Youth Rebellion' poses a serious question for us. How does Samuel know when the dragons were born in? Unless he has gone ahead and talked to someone about the dragons and who else would he ask other than Rhaenerys Blackfyre and her siblings? We know Samuel stayed in Neropos for much longer-' He spent the remainder of 897 AC in Neropos' so why would a high born knight like Samuel live the rest of the year in the city of Neropos and not attempt to get himself involved with the aristocracy of Neropos.
He had should have residence in Neropos so the authorities should be aware of his status in the city so therefore I conclude that Samuel and Rhaenerys must have been in contact when Samuel was in the city.
2.After Neropos Samuel attempts to journey to Centros, he enters the forests and reemerges exactly one year after entering. he says 'He saw. He remembered.' Whatever Samuel saw was life changing and he clings to that memory calling it his destiny multiple times. Samuel says he got his Celtigan Steel sword from Centros which was 'gifted' to him, it is unclear who gifted his sword to him. The Dryads he barely mentions that theoretically could have escaped to Centros or was it something else? Samuel does not share that information, a characteristic of his. Withholding information to do with his background. I want to pay full attention to the sword however; Celtigan Steel was the magical metal found deep in Celtigar's volcanoes and after the Doom of Celtigar there were none Celtigan Steel left. The only Celtigan Steel swords around were ancient swords dating back to Celtigar's time so how has Samuel gotten himself a Celtigan Steel sword. It only makes sense that he would recieve the sword from Rhaenerys Blackfyre, the descendent of Celtigar. If anyone would have a Celtigan sword it would be her family and seeing how close Neropos and Centros are geographically it would make sense that he were gifted the sword by her family.
3.Samuel constantly thinks back to Eilleas and Centros, and his "teachings" in particular. He has a mission that he keeps reffering to but never speaks about. 'He also had a mission, one he had forgotten until recently. The pieces are falling to place.'-Samuel 6. There seems only one conclusion to draw from this and that is Samuel is conspiring to bring about something. 'The pieces are falling into place' definitely show that whatever Samuel's plan is, it is working. He again mentions his mission 'It had been an eventful year since Samuel came back from Eilleas but his mission was still in the back of his mind.'-Samuel X. Again he mentions Eilleas and where were one of the last places Samuel stayed in Eilleas before coming back? Centros and Neropos. Therefore I suggest that Samuel is working as an agent for Rhaenerys and his mission is to gather intel and spy on Aeyron and his court. Samuel even confesses that he won't return to King's Landing after the end of the war- '“You know, I don’t know. I think I’ll stay around the country for a bit and stay here.” Samuel confessed'-Ignis X. He then further tells Ignis ' “I’ll come back but I don’t know when”'.
Why else would Samuel leave King's Landing, leaving behind all his close friends behind. He clearly has fulfilled his mission to Rhaenerys and serves no more purpose to stay at King's Landing, by telling Ignis he will come back, the king and his men will not worry about Samuel allowing him to freely leave to rejoin Rhaenerys. His promise of coming back is true, he just means that he will come back to King's Landing with Rhaenerys Blackfyre and her army. However he doesn't know when because he nor the reader know what Rhaenerys is doing right now.
4.Why would he join Rhaenerys though? Why not, Aeyron threw him under the bus when Samuel had his affair with Nestor's betrothed. He was the king and could have easily kept Samuel in King's Landing. Being exiled in Eilleas, an unfamiliar land, and fighting all the time would fuel his anger at Aeyron. So when he finds Rhaenerys who provides him with a path to revenge he would surely take it. Samuel, himself, knew that Aeyron's pardon would eventually come which would beg the question to Samuel, why hadn't Aeyron pardoned him earlier? Since his return as well Samuel has hated being in Cephri-'he was back in Cephri was again and he hated it.', he obviously prefers the life he had when he was in Eilleas.
In conclusion Samuel is working for Rhaenerys Blackfyre, scouting Aeyron and his forces.