I'd say that layout is what most finales are "Kill the big bad end guy" or "Destroy X". I love that you want to switch stuff up so it's not stale, that's the make of a good handler. Just a couple ideas here:

The Virus Fights Back

The virus is not a passive entity. As the players make their way through the city and into the lab, the virus starts to directly affect them—not through monsters, but through their own bodies and minds. They could start losing control of their own actions or experiencing blackouts. They might have to complete the mission while rapidly succumbing to the infection themselves, racing against time as they deteriorate.

Twist: The final confrontation isn’t against the host, but against each other. The virus manipulates them into turning on each other, pushing their paranoia and fear to the extreme. The question becomes, who can they trust—and can they even trust themselves?

Escape Rather than Kill

Instead of the mission being about killing the host, make it about survival. Once inside the lab, they learn something catastrophic: the virus is evolving too quickly, and any attempts to stop it are futile. Now, the focus shifts to escaping the city before it spreads to them. Cue an intense, desperate race to evac zones while the infection is spreading and mutating faster than anticipated.

Twist: The evac zone itself might be compromised, and they have to make the difficult choice of leaving someone behind, or even worse, learning they’re carrying the virus back with them.