Using a transient regime approach, we explore atomic two-photon spectroscopy with self-aligned homodyne interferometry in the $Lambda$-system. The two light sources at the origin of the interference, are the single-photon transient transmission of the probe, and the slow light of the electromagnetically induced transparency, whereas the atomic medium is characterized by a large optical depth. After an abrupt switch off of the probe laser (flash effect), the transmission signal is reinforced by cooperativity, showing enhanced sensitivity to the two-photon frequency detuning. If the probe laser is periodically switched on and off, the amplitude of the transmission signal varies and remains large even at high modulation frequency. This technique has potential applications in sensing, such as magnetometry and velocimetry, and in coherent population trapping clock.