Clinicians and close partners of people with DID recognize a specific experience: a presentation that is, in every observable respect, a known alter with the same name, self-concept, and relational orientation, yet lacks access to a bounded portion of that alter's episodic history, with no behavioral signal of difference and no self-awareness of the discontinuity. This phenotype has no name or theoretical framework in the peer-reviewed literature. This paper proposes intra-alter substructure: the claim that a named alter may function as a broad cognitive schema whose sub-presentations are state-dependent instantiations, each carrying a bounded episodic memory archive, selected by polyvagal safety appraisal below conscious awareness. A three-layer model distinguishes sub-presentations by behavioral detectability, degree of self-awareness, and depth of episodic discontinuity. The framework synthesizes structural dissociation theory, Putnam's discrete behavioral states model, schema mode theory as applied to DID, and Porges' polyvagal theory, with Kluft's (1988) observations of isomorphic MPD and epochal division as the primary clinical anchor. Case vignettes from eight years of longitudinal naturalistic observation in an intimate partnership are presented as lived-experience corroboration. The primary clinical implication reconceptualizes integration: not the forced merger of named states, but the gradual convergence of sub-presentations under sustained relational safety. Keywords: dissociative identity disorder, alter substructure, schema mode theory, polyvagal theory, structural dissociation, state-dependent memory, intra-alter, parts-based therapy, relational safety