This work presents a rigorous analysis of central modular phases in finite-dimensional Tomita–Takesaki theory and develops an explicit construction of the non-standard case in which the modular conjugation fails to be involutive. Focusing on the four-dimensional Dirac spinor algebra, we show through direct computation that the corresponding charge-conjugation operator squares to minus the identity rather than the conventional plus identity assumed in standard modular theory. Interpreting this operator as a modular conjugation demonstrates the existence of a modular structure whose square equals negative one, providing a concrete counterexample to the usual assumption that modular conjugations must be involutions.

We prove that this sign is a genuine algebraic invariant: modular conjugations with positive and negative square values cannot be related by any unitary similarity transformation, and therefore represent two fundamentally distinct modular phases. We further show that these two possibilities exhaust all central modular phases in finite-dimensional fermionic systems, yielding a complete binary classification. The construction is fully explicit, representation-independent, and formulated within the standard algebraic setting.

Finally, we extend the analysis to pseudo-Hermitian quantum systems by defining a twisted Tomita operator that respects closability and admits a well-defined polar decomposition. This establishes that non-standard modular phases persist in modified inner-product settings and remain compatible with the general modular framework. The results provide a mathematically controlled foundation for modular structures beyond the Hermitian paradigm and contribute new algebraic invariants relevant to modern mathematical physics.