The "Invisible Watchers", or the Invisible or Unseen Observers as they are called in the novel, is a group of legendary god-like creatures in the Metro. In reality they are remnants of the Russian Government that are responsible for manipulating the events of the entire Metro series for the sake of population control and influence over the people.
In the Good Ending of Metro Exodus, Artyom states that the new home for him, Anna and the rest of the Aurora crew is far too big for them and the Order is meant to save all people, heavily implying that Artyom and the Order now plan to take the fight to the Invisible Watchers to liberate the people of the Moscow Metro.
The Invisible Watchers are a legend among the Metro inhabitants. The legend says that they roam Metro-2, observing and directing the Metro inhabitants' every move. A Nazi soldier can be heard talking about Metro-2 and the Invisible Watchers in the Black Station. Ulman also pulls a joke about them on Artyom and Miller while in D6.
"During Ragnarok, the last battle of the gods, the Soviet Pantheon would take shelter in Metro-2 if the forces of evil should prevail. The Metro was made for the sheep (the metro inhabitants) and Metro-2 was made for the shepherds (the Invisible Watchers) and their dogs. At the very beginning, when the shepherd had not yet lost their power over the sheep, they ruled from there; but then their strength gave out and their sheep ran off. The Gates to Metro-2 was closed forever on a place that now covers the map with a blood-red scar. Those who lived in the Metro forget about Metro-2. But even though the gate to Metro-2 was closed it certainly did not stop existing. On the contrary it is all around us. Its tunnels wind with our own. Their stations behind the walls of our stations. The two Metros are inseparable. And those who believe the shepherds could not abandon their herd, say that they are present, directing our every move. And that is the legend about the Invisible Watchers." - the legend of the Invisible Watchers, according to the Nazi soldier found in the Black Station.
The Invisible Watchers are remnants of the pre-war government, or Central Metro Command, having escaped to Metro-2 during World War III. They are the 'shepherds' ruling over the denizens of the Metro.
They are mentioned in Metro 2035 during the conversation between Artyom and Aleksei Feliksovich Bessolov in Bessolov's bunker. In this conversation, the truth about the metro and its factions is revealed: the Red Line, Hansa, Polis, and the Reich are all puppets (or "dummies", as Besselov puts it) of Besselov and the Watchers, who control all of the factions from behind the scenes. Wars fought between the four factions are used as a manner of "controlled conflict", essentially, population control.
In Metro Exodus, during a few of the Spartan's escape from the Metro, Miller speaks of having been directly contacted by the Invisible Watchers. The Invisible Watchers claimed to be remnants of the local Moscow government and receiving orders from the Russian national government's Central Command at the "Ark" facility. The Invisible Watchers maintained that the war had never ended, calling the Spartan Order the "Moscow" unit of the Russian Special Forces, and that NATO forces had occupied most of Russian territory since the bombs fell. They told Miller that this information was highly classified, and that he would be executed as a traitor of the nation if he told anyone, even his own soldiers. Miller states that the Invisible Watchers ordered the construction and maintenance of the radio jammers, ensuring that "NATO" could never find the Metro.
After exploring the surface, Miller and the other Rangers discovered that NATO forces had not occupied Russia and that the "Ark" had never been in contact with Moscow (as the "Ark" had never held the Russian government, instead being a den of cannibals). Miller comes to the conclusion that the Invisible Watchers had created their story in order to manipulate the Rangers through Miller himself. The reality was the jammers were made so that no citizen of the Metro would know that world had not been completely wiped out. The Invisible Watchers had actually been leading all factions in the Metro through similar actions of misinformation, either making them paranoid of further NATO attacks or keeping them too busy fighting one another to ever realize the Invisible Watchers control of the Metro. Thus allowing the Invisible Watchers to live in comparative luxury and security at the expense of the rest of the Metro.
Upon seeing the fate of the Novosibirsk Metro, Miller came to understand the true purpose of the Invisible Watchers manipulations. Novosibirsk Metro's human population had been completely wiped out (save for a single young boy) in a massive two sided civil war, between its leaders and the larger population, over an overtaxed and dwindling medicinal resource. The handful of humans who survived the civil war were picked off by the mutants lurking in the Metro. The Invisible Watchers had done the exact opposite. They kept themselves secret so that the larger population (who were often angry at the hard, dangerous, and often short life in the metro) would not have an easy target to vent their frustrations toward and rebel against. The Invisible Watchers had split the Moscow Metro into the 4 main factions (Hansa, Polis, the Red Line, and the Fourth Reich) to keep the population's attention split and give no easy scapegoat for the Metro's problems. The Invisible Watchers had instigated regular inter-faction conflicts in order to regulate the overall human population of the Metro, striking a balance where the population was large enough to defend itself against the various mutants and other threats in and around the metro, yet small enough to not overtax the limited food/water/medicinal resources of the metro. Lastly, the Invisible Watchers set up the series of radio jammers to make sure no large outside bandit or otherwise hostile group could find the Metro and attack (or otherwise upset the delicate balance in the population numbers). The seemingly horrendous actions carried out by (or most commonly under the indirect orders of) the Invisible Watchers had not been for their own gain, but instead had ensured that the human population as a whole lived and to an extent thrived in the Metro, instead of being completely wiped out.