Site Protection Measures under the Article 6 of the Habitats Directive
Assessment of plans and projects and compensatory measures
Nevertheless, alternatives must be examined if it cannot be ruled out immediately that they were capable of amounting to alternative solutions. This requires a comparative assessment of alternatives. Generally, by examining an alternative, the specific proportionality test must be applied.
The appreciation of conditions for derogation depends on a proper assessment under Article 6 (3) – alternatives can only be chosen if impacts are known and balancing other interests with impacts on the site requires precise knowledge. 
In the case of special circumstances allowing the Member State to go ahead with its project, it must take appropriate compensatory measures to ensure that the overall coherence of the Natura 2000 network is protected. Appropriate compensation can only be put in place when it is determined in the light of the impact. Compensation must specifically address the adverse effects.
The compensatory measures constitute measures specific to a project or plan, additional to the normal practices of implementation of the ‘Nature’ directives. They aim to offset the negative impact of a project and to provide compensation corresponding precisely to the negative effects on the species or habitat concerned. The compensatory measures constitute the ‘last resort’. They are used only when the other safeguards provided for by the directive are ineffectual and the decision has been taken to consider, nevertheless, a project/plan having a negative effect on the Natura 2000 site.
Further reading: The Commission has set up a number of general interpretative and methodological guidance documents on specific provisions of Article 6 in order to provide a better understanding and correct application of the Article.