The Apollo Lens is the final location in the main game (excluding the optional islands) and is where you fight the final boss, the Chaos Chimera.
It resembles an enormous cannon once fully activated, and prior to that, one can only assume that the satue situated in the center of the area is meant to invoke Apollo, the Greek god of the Sun.
The Apollo Lens serves as the final plot point of the game, figuring into the second half (the first half being everything up to the activation of Luna Tower). An ancient and fully operational 'cannon' of sorts used to end the nightmarish Grave Eclipse inflicted by the Luna Tower, in turn activated by the functional Alchemy Dynamo under Belinsk. According to game lore, it was crafted prior to the seal on Alchemy by the Jenei and the beastmen of the day. The Umbra Gear, a set of equipment necessary to managing all of the pure light energy bombarding the facility, was specifically tailored to beastmen laborers on this project so that they would not perish during construction. It is here that the Sol Blade of Golden Sun: Dark Dawn is acquired, serving to open locks on doors featuring a sun motif both in the Apollo Lens and other locations in the areas of Weyard accessible to Matthew and company.
Another potentially important point is that Blados and Chalis were indeed planning on aiming it at a variety of different places. Among the locations mentioned were the seat of Tuaparang itself and whatever remained of Sol Sanctum. One can only assume that they intended to betray the High Empyror of Tuaparang in their attempted abuse of the lens.
After Matthew and his party climbed the Endless Wall and got to the Apollo lens, Blados, Chalis and their soldiers appear. Arcanus tells us that they belong to the Umbra clan. After the Chaos Hound is defeated, Blados, Chalis, and The Chaos Hound merge to form the Chaos Chimera. After defeating it, you find out the Chaos hound was Volechek. Matthew and Sveta are about to die to save Weyard, but Volecheck pushes them both off and sets it off, dying in the process.