LightPhoenix said:
Killing all of them!
I think there's a lot you can do with the idea without having someone get captured. Honestly though, without some thought into the matter, I can't offer any on the fly. And that's why I'm not a writer.
But I am (a writer that is). So let's call this "Cloak and Dagger".
Archer and company approach the "facility" knowing full well what the deal is. The Xindi-Sloth perhaps have the base camouflaged as something ordinary (the local Coca-Cola plant) because to do otherwise would be an invitation for other nefarious Expanse-races to jump on some super bio-tech. The X-Sloth play it cool and escort an Enterprise delegation around the facility to assure them that no fowl play is present. The away team makes some discreet scans to learn the truth about the facility (and discover some vital weak spot in the process).
Meanwhile, the X-Sloth concoct a devious nerve agent to introduce to Enterprise's life support system. To get on board, they fake needing medical supplies. Perhaps these Xindi bump into Trip as he works on the Xindi gun (which I believe is the B-plot in this episode). This would be a tension-filled scene where Trip confronts the Xindi while they irritatingly deny any knowledge of an attack on Enterprise or Earth. "You cannot hold our entire race responsible for the actions of a few, can you?" says one of the Xindi (tongue-in-cheek since they apparently want to destroy Earth for the actions of a few humans...just theorizing here). The Xindi move to guest quarters to set up the virus.
The away team of Archer, Reed, and Hayes devise a plan to knock out the aforementioned "weak spot" in the facility which would bring it crashing in on itself. The Xindi-Sloth on the planet have left that area suspiciously unguarded, but the opportunity is too tempting for the crew to pass on. The away team is not killed outright since the Enterprise would easily lay waste to the facility from orbit (Xindi have no attack vessels here)...
On the Enterprise, Hoshi intercepts a message from the Xindi on board the ship. They tell their superiors on the planet that the virus is ready to be released and will be done as soon as they leave the ship. Hoshi tells T'Pol, who moves with a security team to detain the Xindi (citing the aliens skipped "a medical examination when coming aboard, which is standard practice on Enterprise"). Caught red-handed as T'Pol and company enter, the Xindi activate their virus device and fight their way toward the docking port their ship is waiting at. The Vulcan tells Hoshi to advice Archer of their status...
...As Archer, Reed, and Hayes skulk to the weak spot atop the highest tower of the facility, the message from Enterprise is garbled. "Xindi have released....virus...moving to...quarantine..." The garbled communication comes from the weak spot itself, which turns out to be a power distribution point for the facility. By overloading it, the base will be out of business. The trek to this point continues to be void of security, which only puts the heroes more on the alert. The mystery is solved when the team is attacked by Xindi-Avians (which were rumored to be introduced tonite). The bird bugs are blasted and the mission is a success as the power is set to build up to destruct level. Alarms blare immediately after the sabotage and the Xindi evacuate the area.
On Enterprise, T'Pol orders the deck's environmental systems be sealed so the virus does not escape that area. She also orders Travis (because he needs something to do to) to release the docking hatch on the Xindi's ship so it floats off into space. The corridors leading to that air lock are ordered cleared so no one gets taken hostage. When T'Pol and a heavy security contigent reach the docking port, no one is in sight, the air lock door sealed. With weapons readied, the door is opened with dramatic flair...and the Xindi lie dead inside. Each came aboard with a neuro-toxin to imbibe in case of capture for a quick death. Not too absurd given the nature of their work on the planet.
As the facility blows sky-high, the Xindi-Sloth are given "the speech" by Archer (we are not your enemy, where is the primary weapon being built, etc). Since they know they are defeated and they are not warrior-type Xindi, the Sloth listen meekly, claiming they are only following orders. While a blow has been dealt to stop the Xindi threat, the main base where the weapon is housed must be found. And although these Xindi do not know this place's location, they provide the next breadcrumb for the Enterprise to follow.
Hmm, sorry that was a bit long.
EDIT: Phlox says that the contained virus is not persistent and should dissipate harmlessly within a week's time.
