To help the pair reach their joint goal of running the best atelier, Suelle creates the Ambitions Journal where she tracks everything they need to accomplish along the way. The ambitions listed in their journal contain tasks related to the key pillars of the Atelier series: alchemy, synthesis, battle, and character relations.
As these are completed, Important Quests are unlocked, which will raise the twin’s Atelier Rank upon their completion. This rank is extremely important for young alchemists as chances of discovering new paintings increases the more they level up their Atelier - and opening up the opportunity to undertake the ever-necessary alchemy exam, a Promotion Test.
Throughout their adventures in Atelier Lydie & Suelle: The Alchemists and the Mysterious Paintings, the twins will find a bounty of resources which will be needed to create incredibly useful items. Synthesising items is a necessity for the twins to perfect their skills, as they train to run the best atelier in the country. The Synthesis system has been tweaked with the addition of Enhancing Agents, making the learning process easier for aspiring alchemists. The newly introduced Enhancing Agents attach new effects onto synthesised items and, depending on the agent used, will change the synthesis panel in unique ways.
Change Agents cause coloured tiles to transform into the color of the agent, while Colour Adjacent Agents turn the chosen tile and those next to it into the same colour. Additionally, Connect Agents change all of the tiles connected horizontally, vertically and diagonally to the chosen square into the same colour.
Colour All Agents causes all tiles of the same colour to transform into the colour of the agent. Carefully utilising these agents at the right time can ensure synthesised items are even more effective. For example, bombs can have a wider explosive radius and perform more damage; while health items will have stronger healing properties.