I'm not entirely sure. 'Nickolas' is a name, but the connection to 'first and second story' is very unclear without more context. It could potentially refer to something related to Nickolas and two different levels or events in a story, but that's just speculation.
I don't know. It could be some sort of code or very specific jargon within a particular group or community. Maybe 'Nickolas' is a term for a starting point and 'first and second story' are sequential elements related to it, but this is pure speculation.
The plot could revolve around Harry's apprenticeship under Nicholas Flamel. Harry might be chosen because of his unique connection to Voldemort. Flamel could see that Harry has a special destiny and decides to train him in the ways of alchemy. This could include learning how to transmute substances, understand the properties of magical elements, and use alchemy for defense and offense. Harry could also learn about the history of magic through Flamel's eyes, which is much longer and deeper than what he has learned at Hogwarts. There could be a lot of adventures where Harry uses his newfound alchemical knowledge to fight against the forces of evil.
In this kind of fanfiction, Harry Potter might gain access to the Flamels' vast knowledge of magic. Maybe he would learn ancient spells and potions that are not taught at Hogwarts. He could also be protected by the Flamels' powerful magic, making him safer from Voldemort and his Death Eaters.
Obviously, Harry Potter is one of the most important characters. Then there are the Flamels. Nicolas and Perenelle Flamel are central as they are the ones adopting Harry. Dumbledore might still play an important role as he has a connection to Harry and also to the Flamels in the wizarding world. Voldemort would also be important as he is Harry's main enemy, and the change in Harry's situation due to the adoption could affect their ongoing battle.
For 'Seed of Destruction', the main feature is the origin story. It has great art that sets the tone for the whole Hellboy series. 'The Conqueror Worm' has a feature...
One common theme is mentorship. Since Celestia is an important figure in the MLP world and Spike is a young dragon, stories might focus on her guiding him. Another theme...