One of the key features/characteristics of Habermas’ long oeuvre is his constant attempt to go beyond empiricism and idealism/ naturalism and anti-naturalism. Empiricism and Idealism as well as naturalism and anti-naturalism are to be taken in the broad sense of the terms.
Habermas’ purpose has always been to combine the ‘empirical’ and ‘transcendental’ in his constant effort to go beyond transcendence-less empiricism and highflying idealism. The project is in fact a continuation of Kant who was on of the first in modern philosophy to combine rationalism and empiricism through his transcendental/empirical project (hence transcending empiricism rationalism dichotomy). However Habermas wants to do this without reproducing the two-world dichotomy Kant ended up with. Kant, as Habermas reads him, on the one hand posited a world of pure intelligibility (the realm of necessity, transcendence and unconditionality) and on the other hand he posited a phenomenal world (the realm of contingency, natural and conditional). Habermas’ overall position is naturalist (as against Kant for example) in the sense that he wants to preserve the Kantian distinction between ‘empirical’ and ‘transcendental’ however without reproducing the two world dichotomy. In other words, Habermas wants to incorporate the Kantian distinction in an overall naturalistic picture of the world (in the broad sense of the word natural).
Habermas’ another great model is Marx in this respect. Marx on the one hand rejects idealism fiercely and ferociously and puts forward a position that is thoroughly materialist and naturalist. However Marx retains certain anti-naturalist premises of idealism, such as his notion of human action as a truly creative force rather than an adaptive mechanism. However Marx wants to reformulate these anti-naturalist premises within an overall naturalist and materialist position. Thus Marx tries to overcome the naturalist anti naturalist dichotomy within an overall naturalist position, so he wants to arrive at an overall naturalist position however the one which is compatible with certain idealist insights about the necessity of explaining the spontaneity of human action and rationality in non reductionist terms. Habermas agree with Marx in this aim however he does not think that Marx ever achieved his goal.