With advances made in the fields of energy generation from renewable sources, airborne electrical propulsion, and autonomous system operation, much activity has been directed towards the development of so called high altitude pseudo satellites (HAPS) in recent years, with Zephyr (Airbus) and Aquila (Facebook) as prominent examples. Compared to classical orbital satellites, these are designed to require lower deployment costs and to offer a high flexibility in operational tasks and a long mission endurance. In the project StraVARIA, the goal was to develop a high-fidelity multiphysical simulation of such a HAPS, including a long-term mission planner, a reactive guidance system for weather avoidance, a flight control system with protections, a 6-DoF model with solar-electric propulsion system, and a comprehensive environment simulation with 4-D wind and turbulence. Due to the long mission duration, the mission planner and guidance system offer an increased autonomy level compared to standard operator controlled UAVs, however human input is still required for high level planning. The acausal and object-oriented modeling language Modelica has been used to create the integrated simulation model, enabling a modular and detailed modeling approach. By automatic code generation and optimization, simulation efficiency is improved, which is an important factor when considering long-term missions. Results of the integrated simulation show that missions like area surveillance and communication relay are possible whenever adverse weather conditions can be avoided. Ascending to and descending from mission altitude of approximately 18 km also poses a threat to the lightweight HAPS construction since layers of stronger winds and atmospheric disturbance have to be passed. To this end, simulated example missions over Bavaria are presented showcasing these effects, where mission success is ensured by means of the long term mission planner, the reactive guidance, and the inner-level protections implemented in the flight control system.