We demonstrate a novel low-cost photonic-layer secured communication system that incorporates intensity modulation direct detection (IM/DD) scheme with a 4-level pulse amplitude modulation (PAM-4). In the proposed system, the signal is buried under an amplifier's spontaneous emission (ASE) noise and coded with a spectral phase mask. As a result, the signal is stealthy and encrypted in both frequency and time domains. We analyze the reception performance of the secured signal under direct detection, and analytically compare its SNR with a conventional PAM-4 system, demonstrating that only an eligible receiver achieves a decryption of the stealthy and encrypted signal. Furthermore, we experimentally validate these findings showing a significant processing gain, which allows an error-free reception, despite a negative optical-SNR.