This dataset contains the optimised PyPSA network files (.nc format) for the nine scenarios modelled in Geis et al. (2026), published in Applied Energy. The networks cover Germany's pathway to climate neutrality across three investment periods (2025, 2035, 2045) and four flexibility scenarios (LowFlex, LowBattery, Base, HighFlex). Each network file contains the full sector-coupled energy system model of Germany and its neighbouring countries, including optimised investment and dispatch decisions for electricity, heating, transport, hydrogen, and synthetic fuel sectors at hourly resolution. The model is based on PyPSA-DE, an open-source sector-coupled energy system model built on PyPSA-Eur and PyPSA. The code to reproduce the model runs is available at: https://github.com/JulianGeis/pypsa-de-flex/tree/feature-flex