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Conceptual aircraft design is traditionally an expert-mediated iterative process in which a human designer proposes a configuration, runs low-order physics, inspects the result, and re-proposes. We present AlphaJet, an end-to-end automated synthesis pipeline that closes this loop. From a textual mission specification (mass, range, cruise speed, hard size envelope, engine count, areal density) AlphaJet evolves a feasible 3D aircraft in real time, scored by a transparent multi-disciplinary fitness function covering aerodynamics, structures, weights, stability, packaging, and geometric mount consistency. Three contributions distinguish our approach: (i) an Anatomically-Disentangled Variational Autoencoder (AD-VAE) whose first 25 latent dimensions are supervised to align with named anatomical parameters, providing an interpretable shape prior; (ii) a topology-elitist genetic algorithm that protects the best individual from each of five tail topologies and triggers stagnation restarts, preventing premature collapse to a single configuration; and (iii) mount-aware geometric scoring that computes signed penetration between engines and other structural parts, eliminating the redundant artifacts common in generative aircraft models. The full loop runs interactively on a CPU and streams every generation to a browser viewer, making it a practical real-world automation tool for early-phase design-space exploration.