In the framework of the European project CORTEX, included in the H2020 program, the experimental campaign carried out with the CROCUS reactor, at the École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland, aims at setting up methodologies and tools for the analysis and the interpretation of neutron noise in view of their industrial applications. An important part of the CORTEX project deals with code development and validation. In this paper, a new methodology for the simulation of neutron noise has been formulated and implemented in the APOLLO3 code. The method is based on an improved point-kinetics model employed in a fully heterogeneous 2D transport calculation. In this work, the theoretical derivation and the successive validation of the model are presented, comparing the Cross-Power Spectral Densities (CPSD) of measured and computed detector responses. Future work will consist in extending the application of the method to the analysis of 3D configurations, in particular for full reactor studies.