Integrating the IFF with the Normandy is tricky. Until the job is complete, the team (which means all companions) must travel by shuttle. This is a storytelling way of removing certain people so that the unnamed crew, and some of the background characters, can be captured without changing the gameplay.
While Shepard and the other fighters are away, a Collecter ship attacks.
In the IFF is a virus that even the AI EDI couldn’t detect. She can’t defend the Normandy. It’s up to Joker, the pilot with brittle bone disease, to help.
It’s a clever sequence, where the player drives Joker with his limp from the bridge to engineering. Around him are Collecters harvesting the rest of the people on board. He’s able to patch EDI back into control. She tells Joker she will seal off his section of engineering and open the rest of the ship to vacuum in order to clear out the Collectors. Joker asks, “What about the other people?” “The crew is gone, Jeff.” The entire ship’s crew — the cook, the yeoman, the cute engineers — has been captured.
After this, Shepard and our teammates return. We now have a choice: Immediately go through the Omega 4 Relay to rescue our people, or wait in order to strengthen the team. In gameplay terms, this means that two teammates haven’t completed loyalty missions yet and will be vulnerable to dying during endgame. The Normandy attack is automatically triggered when Shepard reaches this point, so it can’t be avoided. If she helps two teammates, the captured crew will not be saved. If she helps one teammate, half the crew will not be saved. It’s a vicious trade-off.