A self-assembled binuclear coordination cage of the Pd2L4 formulation has been constructed by complexation of Pd(NO3)(2) with N,N'-bis(3-pyridylmethyl)-naphthalenediimide (L). The cage, i.e., [Pd-2(L)(4)](NO3)(4) (1), displayed a further self-assembly phenomenon to afford a gel phase, upon dissolution in either dimethyl sulfoxide or acetonitrile-water (1:1) followed by standing at room temperature. It was observed that a synergy among the metal ion, ligand counteranion, solvent, and concentration played a vital role for metallogel formation. The morphology of the metallogel as observed from microscopy studies revealed the formation of a rare variety of nanoscale metal-organic particles. Salient features of the gel include the thixotropic (mechanoresponsive) nature, in addition to the reversible chemical-stimuli-responsive behavior. The presence of naphthalenediimide moieties at the backbone of the cage and the cationic nature of the cavity of the cage could be exploited to study the functional aspects of the gel. The porous gel exhibited the abilities to uptake pyrene as a guest and to selectively remove anionic dyes from aqueous solutions. The gel could bind representative anionic dyes like "acid blue 93" and "methyl orange" in the absence or presence of certain cationic dyes, making the material suitable for selective dye removal applications.