The Zephyr One is the aircraft that Director Phil Coulson and his revived S.H.I.E.L.D use as a mobile command platform for their operations. The plane was designed and built by Leo Fitz and it is what Coulson has used to replace the old plane (S.H.I.E.L.D 6-1-6) after it was destroyed by Hydra.
The Zephyr One was first seen in S.O.S. Part Two when Coulson prints out the blueprints for the airplane. Coulson tells Andrew about the designs and that he has Fitz working on it. By the start of season 3 the Zephyr One was complete and combat ready
In "Maveth," Mack orders everyone to return to Zephyr One and if Hydra breaks through their barricades or if Hive comes through the Monolith portal then they need to fire every missile Zephyr One has at the castle, regardless if Mack is still inside or not.
In "Ascension," Hive takes control of Zephyr One with the plan of first flying the jet to a high enough altitude and then detonating the warhead containing Radcliffe's pathogen which'll turn million of humans into Primitive Inhumans. However, Coulson first uses a quinjet to board the Zephyr with the others, then distracts Hive with hologram of himself, and with Hive distracted they retake the Zephyr and load the warhead onto the quinjet before it detonates.
This new aircraft can stay in the air much longer than the old one. Days, really, so rapid response anywhere is..."
"You love your new toy don't you?"
"I very much, love my new toy"
-Phil Coulson and Daisy Johnson
Zephyr One is a highly advanced aircraft that is capable of staying in the air for weeks (6 weeks maximum time on) without refueling. The plane has a room where the Containment Module leads which is made of some poly-tectic adaptive materials as the module which means it can be adapted to counteract powers such as that of an Inhuman.
Like the Bus, Zephyr One is capable of generating a cloaking field thereby making it invisible and it has a docking platform on the roof for smaller aircraft like quinjets to land on mid-flight.
- It is shown that Coulson likes this new plane, maybe even more than the old one.