Applied Phlebotinum: Earthstone, an Earth-based variation similar to Kryptonian Sunstone, but much more dangerous, and capable of disabling large quantities of technology. And, as shown by Issue 6, anything its affected cannot operate under the commands given by it after it is brought a select distance away from Earth.
Badass: In addition to Superman, we have Wraith, who is stronger, faster, and more durable than he is, and absorbs far more solar energy.
Came from the Sky: Wraith, not unlike Superman. Unlike Superman, however, he landed near a military installation, rather than near a farm in Kansas.
As usual, Batman proves to be this, having developed a Batsuit against Superman's Super Senses before he truly trusted him. He's been considering destroying it, but Superman always tells him not to, just in case it proves necessary to stop him.
The U.S. military under General Sam Lane has been working on "black hole" technologies to fight Superman. These include "max-grav-photon-emitters", a.k.a. "black hole lasers", and "black hole bullets", which are 50 caliber rockets with light vacuums inside of them.
The Russian military has also been working on anti-Superman technology, specifically the "XR" drones. These unmanned drones have shielding that protects them from Superman's Heat Vision and Super Senses, as well as firing bullets that emit red sun radiation just before impact to be able to pierce Kryptonian skin and armor.
Dissonant Serenity: Luthor calmly monologues on the history of origami while Jimmy Olsen (who he kidnapped as part of a plan to kill Superman) screams at him to stop the machine working on his hand.
Driven to Villainy: Wraith laments that this will happen between him and Superman, with him being forced to take him down. In Issue 6, he abandons this, instead going for revenge, but more against Batman than Superman.
E.T. Gave Us Wi-Fi: Apparently, large quantities of technology since 1938 comes from the use of the alien equation by the Machine. The culmination of this is Earthstone.
Foil: Wraith serves as one to Superman, being a similar superhuman who is, rather than working alone, almost completely under the grasp of the U.S. military, and has a My Country, Right or Wrong mentality, in contrast to Superman's more internalized moral code.
Fun with Acronyms: Wraith's name is one. It stands for William Rudolph's Ace In The Hole.
Good Versus Good: Barring Ascension, both sides of the conflict in the comic are ostensibly good. Superman is as he usually is, but Sam Lane just wants to get US government property (Earthstone) to better protect the United States, and Wraith is a reluctant villain. Eventually subverted on that last part, when Wraith begins to break down and goes after Batman for revenge, not because he was told to.
Government Conspiracy: The Machine, home of Wraith and many alien technologies that have been incorporated into human operations. It was formed by Franklin D. Roosevelt in 1938, and has been a major force for the military ever since from behind the scenes.
Benevolent Conspiracy: The goals of this conspiracy are to dispel danger zones, rather than enforce will. In essence, it militarizes a Superman.
Hero Antagonist: Although he did perform horrible actions (such as destroying Nagasaki, a civilian population), Wraith seems to genuinely believe in the peace and safety of Earth, and is reluctant to hurt Superman. That said, their interactions are heating up considerably over time.
Kryptonite Ring: With a twist. Superman has one made for Wraith's species by Batman to interact with his specific energy signature in Issue 6. In Issue 8, after defeating Wraith, Superman shoves the ring down Wraith's throat.
Muggle Power: The goal of Ascension is to destroy the Machine with its own technology, allowing humanity to develop again separate from alien technology's influence.
My Country, Right or Wrong: Wraith has this mentality for the United States, regardless of the fact that it isn't actually his country, in contrast to Superman, who views justice and peace in more broad terms than a country alone.
My God, What Have I Done?: William Rudolph apparently went through this late in his life for his connections to the Machine, breaking up the equation so that Earthstone could not be found by almost anyone.
Nice Guy: For all of his military work, Wraith appears to be this, sincerely regretful that he might have to kill Superman, warning of possibly confrontations that could come up from him at the behest of the military, and helpful concerning his powers. Even after he was attacked with a Kryptonite Ring, he's still Affably Evil toward most people except Superman.
Self-Destruct Mechanism: In Issue 6, Jonathan Rudolph activates one at Ascension's base, destroying most of the Earthstone, but also most likely killing most if not all of Ascension's members and himself in the process.
Unskilled, but Strong: As Superman explains, the fact that Wraith is a Military Superhero means that he always had someone else to have his back, and thus he never had to truly learn how to fight, especially with his signature cloaking. As a result, when he manages to even the playing field in Issue 8 by forcing the fight into the mantle of the Earth to make Wraith's manipulation of his energy signature nigh impossible, he manages to fight him extremely effectively, since he had to learn how to fight on his own with minimal aid by comparison.
Western Terrorists: Ascension, as shown in issue 5 by the identity of their leader being Jonathan Rudolph, grandson of General William Rudolph of the US Army.
Wham Shot: Shown in the first scene of the first issue, where the Fat Man bomb dropped on Nagasaki is revealed to be actually just a casing for Wraith, who was actually the bomb itself instead of just an inanimate atom bomb.