Clint was in the room where it happened, all geared up and ready for a quick trip back home once Tony sent the All Clear. But the All Clear never came. Every partially garbled transmission sent his blood pressure spiking. His palms itched with the need to move, to have his bow and an arrow in hand from whatever threat Tony was facing over there. And then he heard those doomed words: "Shit. It's New York." His world. Something was very, very wrong with his world, if the sound of Stark's voice was anything to go by. The portal flickered right as Clint took a step toward it. Someone stopped him. Bodily. He didn't know who, didn't care. That was his world, and Tony sounded terrified. Clint started yelling, still trying his fucking hardest to get to the portal, variations on a theme of "Let me go!" and "I have to get in there!" and "TONY!"
But it was for nothing. The portal closed. Tony was gone. And maybe his world was too. Clint staggered to a corner and slumped into it, his head in his hands and not saying or doing anything until someone came to pull him out.
Derek likes Tony well enough, but he'll be more sad on Steve and Pepper's behalf. He'll be wherever Steve needs him to be whenever he gets done with leadership things.
Zari is sympathetic, but knows that the best way to help is to stay out of the way and help around the Facility in whatever limited capacity she can. If Pepper isn't too inundated (after a respectful few days), she'd approach her about releasing a public statement so the company board doesn't get too antsy.
Jemma will help with Team Science in anyway she can. She's still got friends in the new SHIELD agency, and they can crunch numbers while remaining mostly in the dark on what it's for.
Nico just got here, has seen the Avengers on the news, but has no emotional ties to what's going on. RIP Iron Man, I guess.