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I can explain regarding opioids. The human body produces it's own opioids in small amounts, which dock to specific brain receptors (those work like key & lock), which makes us feel good by releasing dopamine and has a slew of other body-wide consequences like changes in core body temperature and slowing down the digestive tract.
Using opiates floods those receptors with more and more fitting keys that stay in the lock for far longer than the body's own opioids. This is an high that is not reproducible by anything else. But it has the consequence that now the body reduces the amount of receptors/keyholes because the reaction was so intense, creating tolerance.
After a short while of usage, the bodys own opioids are not enough anymore to create a meaningful response - the external opioid addition has completely overwhelmed the miniscule potiental of the bodys own signal cascade. Not adding opioids now leads to withdrawal - the gut starts working like crazy and cramps painfully, you feel cold the entire time, you are depressed, your nose runs constantly, and all this time your whole body and mind scream to get the next dose.
It takes a very careful approach to get the opioid system back into balance. Substitution works as an external opioid regulation mechanism, where the "keys" don't fit the lock perfectly, but also get "stuck" there for a while, leading to a lower activation and blocking out any additional opioids from doing their work. After stabilizing, it can take pretty long to reduce the substitution to a level where withdrawal is easily manageable, so that the natural system can take back it's function. People who are predisposed for addictive behaviour might even just keep taking the substitution to prevent relapse.