This paper introduces Fossil 2.0, an advanced software tool designed for synthesizing certificates such as Lyapunov and barrier functions for dynamical systems represented by ordinary differential equations and difference equations. Fossil 2.0 features a range of significant enhancements, including improved user interfaces, an expanded library of certificates, controller synthesis capabilities, and an extensible architecture. These advancements are detailed as part of this paper. The core of Fossil is a counterexample-guided inductive synthesis (CEGIS) framework that ensures soundness. The tool employs neural networks as templates to generate candidate functions, which are rigorously validated using a satisfiability modulo theories (SMT) solver. Key improvements over the previous release include support for a broader class of certificates, integration of control law synthesis, and compatibility with discrete-time models.