In order to understand the cometary plasma environment it is important to track the closely linked chemical reactions that dominate ion evolution. We used a coupled MHD ion-chemistry model to analyze previously unpublished Giotto High Intensity Ion Mass Spectrometer (HIS-IMS) data. In this way we study the major species, but we also try to match some minor species like the CH x and the NH x groups. Crucial for this match is the model used for the electrons since they are important for ion–electron recombination. To further improve our results we included an enhanced density of supersonic electrons in the ion pile-up region which increases the local electron impact ionization. In this paper we discuss the results for the following important ions: C +, CH +, CH + 2, CH + 3, N +, NH +, NH + 2, NH + 3, NH + 4, O +, OH +, H 2O +, H 3O +, CO +, HCO +, H 3CO +, and CH 3OH + 2. We also address the inner shock which is very distinctive in our MHD model as well as in the IMS data. It is located just inside the contact surface at approximately 4550 km. Comparisons of the ion bulk flow directions and velocities from our MHD model with the data measured by the HIS-IMS give indication for a solar wind magnetic field direction different from the standard Parker angle at Halley's position. Our ion-chemical network model results are in a good agreement with the experimental data. In order to achieve the presented results we included an additional short lived inner source for the C +, CH +, and CH + 2 ions. Furthermore we performed our simulations with two different production rates to better match the measurements which is an indication for a change and/or an asymmetric pattern (e.g. jets) in the production rate during Giotto's fly-by at Halley's comet.