Nuclear technologies have a strong potential and a unique role to play in delivering reliable low carbon energy for a future net-zero society. However, to assure the sustainability required for the long-term success, nuclear will need to deliver innovative solutions as proposed in iMAGINE. One of the most attractive features, but also a key challenge for the envisaged highly integrated nuclear energy system is the need for a demand driven salt clean-up system. The work described provides an insight into the interplay between a potential salt clean-up system and the reactor operation in a plutonium started core in a dynamic approach. The results presented will help to optimize the parameters for the salt clean-up process as well as to understand the differences which appear between a core started with enriched Uranium and Plutonium as the fissile material. The integrated model is used to investigate the effects of the initial fissile material on core size, achievable burnup, and long term operation. Different approaches are tested to achieve a higher burnup in the significantly smaller Pu driven core. The effects of different clean-up system throughputs on the concentration of fission products in the reactor salt and its consequences are discussed for general molten salt reactor design. Finally, an investigation of how a plutonium loaded core could be used to provide fuel for future reactors through fuel salt splitting is presented with the outcome that one Pu started reactor of the same size as a uranium started core could deliver fuel for 1.5 new cores due to enhanced breeding. The results provide an essential understanding for the progress of iMAGINE as well as the basis for inter-disciplinary work required for optimizing iMAGINE.