Is Viper relying on one thing to win the day? One superweapon used for blackmail/protection? Allowing Viper to consolidate territory without fear of massive reprisals? "If Greater Viperstan is attacked, the world will feel the might of our CoreCracker bomb!"
How do they expect to hold so much territory? How do they plan to defeat the world's armies/police/other agent groups/supers? What is their edge? An army of super robots? A sudden breakthrough in the Man Mutation Project? Some combination?
Will the world know it's Viper at first? Or will it be a series of seemingly unrelated threats that all coordinate at once?
Here's how I see an example of a serious attempt by Viper to take over after having gotten very lucky and laid serious groundwork. This could be the culmination of decades of work.
1) Viper has a nest stages some big global blackmail plan, which of course fails. Evidence from that nest leads to VIPER HQ! Authorities smash the central HQ, but it is destroyed by massive explosion. From interrogations and telepathic scans of captured agents, the good guys feel VIPER has taken a major blow. (In reality, this was a setup. The first nest was rebellious, and Viper gets it removed without getting its own hands dirty. Info was planted to lead to the "HQ", staffed with a massive self destruct system and agents who really believed they worked at Viper's HQ, so they are effective misinformation even under psionic probing.)
2) Viper itself lies low, gathering its strength. The war via proxy begins.
Various parts of the world blow up over the course of several months. Coups by Viper pawns, local rebellions, economic collapses all secretly staged by Viper. Individual Viper agents may be found with various groups, working with their "new masters" now that Viper itself is "on the ropes". The world's powers get deeply involved in the many world messes, heavily committing their troops/resources etc to the various conflict areas/trouble spots.
3) Now that the major powers are overextended far from home, trouble hits locally. Local villains who have been secretly funnelled resources by Viper strike at the heart of the major powers and their allies. These second-tier threats and the authorities bleed themselves fighting each other.
4) Disaster! The US, Japan, China and elsewhere are hit by a devastating series of earthquakes and tidal waves that stretch resources to a breaking point. (Caused, of course, by Viper's Seismatron)
5) Viper reveals itself. The reason Viper has long avoided trying for magical power is revealed - they have long been in possession of the Six Serpent Stones of Skirax, which in concert can drain most of the magical energy on Earth! Most of the world's mages, magic weapons and such are powerless. Massive EMP weapons hit as well, burning out most high-tech devices that have not had special, specific protections built in (such as Viper's own have). The devices maintain a field around the planet, continuing to interfere with high-tech gear. Viper demands the world's surrender, and several hard-pressed minor countries give in.
6) The assault. Viper agents come out of the woodwork in the major powers, who are still tied up overseas, and have been drained by fighting local threats and disasters. Spearheading the assaults are legions of Viper Warbots and hundreds of previously unseen supervillains with similar powers - the result of a very successful line of Man Mutation Project research. With their high-tech weapons useless, the good guys are hard-pressed to handle them. Viper makes many gains, concentrating on destroying the opposition while they are off-balance. They reason that they will have all the time they need to consolidate control once their foes are defeated. In their wake, Viper leaves devastation, chaos, and anarchy - which furthers their plans and weakens their foes further. Prisons are liberated, and inmates drafted into service in Viper's armies. The tide rolls on...
Possible problems:
Someone gets wind of the plan, causing Viper to reveal itself and strike directly earlier than planned...
Someone links the seemingly separate threats together...
Someone cracks the secret of the Viper EMP protection from a captured Warbot, and begins mass-producing them, enabling the battlesuits, etc of the good guys to function again...
The location of the Serpent Stones is discovered, and the good guys destroy them, enabling magic and magical heroes to work again. Needless to say, every mage on Earth is upset with Viper...
The Serpent Stones are NOT discovered, and an extradimensional magical threat immune to their effects sends a demon army through to invade Earth itself, now that Earth's mages are powerless to stop it...
The new legions of supervillains, having a common origin, have a common weakness, which once discovered makes them much easier to deal with...
...and so on. Of course, once VIPER fails in it's real attempt, the world will crush it utterly. Or so they believe...