In recent years, the EU has been facing more crises than ever before, a trend that most likely will not be broken. Over the last few years, we have seen an economic crisis, migration crisis and a pandemic to name a few. With every new crisis where there is no set agenda on how to act member states are presented with a choice of either take the matter in their own hand and go-it-alone or pursue integration and cooperation. With each member state being able to chose there is potential for the cooperation to become strained. Thus, the purpose of this thesis is to understand the choice of go-it-alone or integration in a context of the nexus of state sovereignty/integration. The nexus will be used to understand the choices of Estonia and Hungary during the Migration crisis and Covid-19 pandemic.  The study was conducted by making use of a qualitative comparative approach of Estonia and Hungary. To engage with the concept of sovereignty four criteria were established from previous theory, Intergovernmentalism and Neofunctionalism. Each perspective was constructed into a pole structured ideal type to allow for analysis based on official governmental material, such as press releases.  The results show that the nexus ’state sovereignty/integration’ can explain the choices made of Estonia and Hungary to either go-it-alone or cooperate. The results show that Estonia was more likely to, in times of crisis, approach integration, but only slightly. Hungary on the other hand was more likely to go-it-alone.