To elucidate the morphological modifications that occur in the cell cortex during trichocyst docking in the ciliated protist Pseudomicrothorax dubius, the cortical ultrastructure of cells with or without docked trichocysts was compared. Additionally, the ultrastructure of the docking sequence was followed in cells fixed when many trichocyst docking events were induced. The P. dubius cortex is not composed of discrete alveolar sacs and alveolar septa as in many other ciliates. Instead, one finds a continuous alveolar space that is interrupted only at certain, specific points such as at the tips of docked trichocysts. Not only is the alveolus absent at the trichocyst tips, but so is the rigid epiplasmic layer. Thus, the docked trichocyst is positioned in pores that penetrate these cortical layers and is attached to the plasma membrane in an exocytosis-ready position. In cells without docked trichocysts, one observes unoccupied docking sites in the cortex; however, the alveolar space and the epiplasmic layer are continuous and intact above the unoccupied sites. Therefore, a docking trichocyst must penetrate the epiplasm and the alveolus before the trichocyst can become attached to the plasma membrane. The localized dissolution of the epiplasm and the membrane fusion during alveolar penetration were followed step by step in serial sections of docking trichocysts, revealing that the cortical modifications at the docking site are induced by a series of direct, sequential interactions between the membrane of the trichocyst tip and specific cortical components.