Buffy-Faith style relationship conflict between the 2 leads?
Another thought entirely – have the disappearing character be the wife / long term gf of the questing character. Have him be also somewhat seduced by the scene. Or just any way to make him a him (lost gf is clichéd and also difficult as too emotionally charged)
Idea of parallel worlds – use the metaphor of parallel worlds – though the second world, the underground world is right there in actual fact, it may as well be magical realm requiring magical portals because most people are so unaware of its existence. Or aware but afraid. An old ruined town under the bright and sunny place? Sewers, tube tunnels, bomb shelters…? Alien ruins? Submerged starship? (too rocky horror?)
Remember the gothic side to it
Remember the funny side to it (it’s so cheesy it had better be funny or nobody will forgive).
If the infiltrators are androids, the aliens could look like anything – cthulus? The alien presence on Earth could in fact be gone; leaving a factory that builds and tracks the androids, which no longer have a master or a purpose. Who cares if it’s cheesy? Nefertiti could have been an android. Cleopatra.
If it’s not Earth, same general idea, easier to invent but loses impact & resonance.
Sub plots needed.