MDMA depletes your serotonin, so your will have lower tone until it is regenerated. After reading about ray's ideas about LSD, i think similar is true with MDMA. The "come up" is described as unpleasant body load. This corresponds to serotonin flood. The desirable effect starts when the serotonin is cleared and/or receptor amount is reduced/desensitized in adaptation to the initial flood, resulting in long-term dampening.
If your problems were from excessive serotonin signalling, you might have accidentally taken a targeted treatment.
MDMA & LSD are way different... I would not compare them like this.