This paper presents results from a new method, ZooM-CiTTy, that aims to accurately reproduce filamentation observed in profiles of chemically active species in the free troposphere. Lagrangian tracer reconstructions of aircraft measurements across pollutant plumes including a stochastic representation of mixing are coupled with photochemical trajectory simulations, initialized with global model fields. The results provide a high-resolution simulation of trace gases along the flight track together with a detailed picture about the multiple air mass origins influencing chemical composition in the region where plume measurements were taken. This paper builds on results from Pisso et al. (2009) for the dynamic part of the model (the stochastic tracer reconstructions) and focuses on reconstruction of reactive species like O3. The model is evaluated for a case of long-range transport of a forest fire plume from Alaska to Europe. Simulated trace species are compared with measurements made in the plume by the DLR Falcon aircraft flying over Europe, and the role of photochemistry in governing the chemical composition across the plume is evaluated. It is shown that the model reproduces well O3 and NOy concentrations and O3 production per CO in the plumes as well as gradients at plume edges. In particular, because ZooM-CiTTy represents the contribution of several air masses to a measurement at a particular location, the model can reproduce so-called mixing lines between air masses. Results show that photochemistry and mixing contributions vary in different parts of the plume and that resulting trace gas correlations are a combination of these different mixtures. One limitation of the method is the fact that mixing between air masses is only performed at the end of the trajectories. Errors on simulated O3 reconstruction from this formulation are evaluated. These errors seems to be negligible in this case (in the free troposphere, far from emission region) because strong gradients are maintained by large-scale winds. Results from ZooM-CiTTy are also used to evaluate errors due to nonlinearities in O3 photochemistry in coarse-grid models. It is shown that in cases where strong gradients are maintained, errors in net O3 production can be as high as 50% at plumes edges. This new method is interesting to simulate relatively small layering structures observed in the free troposphere, but a more realistic treatment of mixing “en route” is needed if the model has to be used more extensively.