Having decided that the alien invaders are too powerful for Nod to take on alone, Kilian Qatar ordered a ceasefire in the A-NZ theater and ordered the Nod Commander to assist the commander of GDI's Sydney garrison in defending the city, much to the anger of Ajay and the rest of the Brotherhood. She justified her decision by saying that if GDI loses its Sydney base, they will withdraw from Australia, and Nod simply did not have the manpower to defend the entire country on its own.
When Ajay accused her of treason, she revealed that she had an ulterior motive for helping GDI: there is a GDI lab containing the release codes for the nuclear warheads they stole, as well as the location of delivery systems. By stealing these information, they would be able to rebuild Nod's nuclear arsenal.
During the mission, events unfolded almost exactly as Kilian expected: the aliens' Devastator warships destroyed sections of the Sydney City Wall, allowing a Nod saboteur to enter the GDI lab and steal the information. However, signal from a mysterious source began issuing unauthorized orders to Nod commanders in the A-NZ theater, compromising their fragile alliance with GDI. The Nod Commander also received one such order through Ajay, apparently coming from Nod Central Command: destroy the ion cannon control center in Sydney.
Regardless, the Nod Commander destroyed the key alien structures outside Sydney, temporarily saving the city.
(This walkthrough assumes Hard difficulty)
At the start of the mission, immediately start building a Tiberium refinery, a shredder turret, two harvesters (one for each Tiberium field) and three saboteurs. Place the refinery near the Tiberium field to the west, and place the Shredder turret there to protect it from alien infantry. The Scrin will mostly focus on the GDI base at first, but will also send shock troopers, Disintegrators, and Seekers to harass your base, so make sure to defend it well.
Once the refinery is finished, build an air tower and an Emissary. Use call for transport with the saboteurs and the Emissary. Move the carryalls north into the Sydney City Wall to avoid alien anti-air fire. Drop one saboteur near the GDI lab and capture it, then move the rest to the nothern Tiberium spikes. Capture the spikes and deploy the Emissary near the Tiberium field.
Back at your base, upgrade all of your power plants with liquid Tiberium core, then build some additional defenses, including more shredder turret near the western refinery, Obelisks to defend your base from vehicles, and SAM turrets for aircraft. Once you have enough funds, build two refineries on the northern Tiberium field to further enhance your economy. Note that there are three squads of Disintegrators near the field, destroy them with shredder turrets.
The GDI base will eventually be overwhelmed, and the Scrin will begin sending Annihilator tripods, Devastator warships, and Planetary assault carriers toward your base. Build a large number of Avatars, Raider buggies, and Venoms to defend your base. Researching the laser capacitors upgrade at the tech lab would also help.
Eventually, the Scrin will destroy sections of the city wall with Devastators. At this point, you will receive a mission to destroy the ion cannon control center inside the wall. Doing so will make the next mission easier. Once you have a steady economy and your base is secure, it's time to move onto the Scrin base.
Depending on how well-defended the Scrin base is, you can tackle it in several ways. If the base is lightly defended, you can simply destroy any defenses with four or five Avatars (preferably upgraded with flame tanks to deal with infantry). Otherwise, you can lure Annihilator tripods into Obelisk range, destroy them, and capture them to bolster your forces. The Scrin will likely build a massive number of Disintegrators, which you can deal with using Black Hands. The storm columns and photon cannons can either be destroyed with beam cannons or simply overwhelmed with Avatars and tripods. Destroy the marked Scrin structures to complete the mission.