HYPNOS in Digimon Tamers starts off as this.

Many of these agencies will claim to be acting in the interest of some greater good, whether they actually believe it or not. Examples of this trope in democratic countries will typically mislead well-meaning politicians, act without proper authorization or oversight, and generally flout the idea of checks on their actions. When they work for authoritarian regimes, expect both kinds to be either acting in accordance with the regime's will or trying to covertly take power for themselves. Domestic-oriented agencies will often frame and entrap those considered undesirable, help criminals for their own reasons, try to blackmail dissidents, and even go so far as to target public officials who stand in their way.

Foreign-oriented agencies will often give help to bad actors abroad, arrange the removal of foreign politicians or even entire governments they don't like, mastermind at least one False Flag Operation, and engage in naked imperialism. These depictions of (real or fictional) intelligence agencies will engage in some very ugly behavior. Add in the facts that many real life intelligence agencies have engaged in morally dubious actions and many events are known or suspected to have involvement from intelligence agencies, and it probably comes as no surprise that intelligence agencies are quite frequently portrayed as corrupt and/or evil in fiction. It's certainly not hard to make villains out of shady puppetmasters manipulating events from behind the scenes or agents of subterfuge secretly gathering information and engaging in subversion. On the other hand, these same qualities have led to spy agencies being portrayed in far less flattering ways. Since intelligence agencies are shadowy and secretive organizations by their very nature, and their field operatives tend to be very clever and stealthy, it's no surprise that their mysterious natures have led them to be portrayed as full of suave, debonair spies and elite, noble enforcers of the law. The espionage profession is often considered to have a certain mystique and glamor to it.

How to be a real spy agent