|“|| I thought we were alone in the universe?!!|
- GDI Soldier when the scrin arrived
It was not until later that it was revealed that Kane had knowingly provoked GDI into using the Ion Cannon to detonate the bomb, which he knew would attract the attention of a Tiberium-based extra-terrestrial race, known as the Scrin. They took this as a sign of advanced Tiberium infestation on Earth, and arrived in force...
Shortly after the Siege of Temple Prime, GDI deep-space satellites picked up motion on the edge of the solar system. This turned out to be a fleet of non-terrestrial ships, headed for Earth at "near-relativistic" speeds. Director Boyle ordered an Ion Cannon strike against the invaders with the entire network of cannons. However, the crafts merely dispersed into multiple smaller craft, landing in Red Zones across the world.
Scrin forces began constructing massive Threshold towers in the world's Red Zones, for still unclear purposes. At the same time Scrin forces began attacking major population centres - GDI and Nod alike - with a ferocity unmatched before or since. Shock troopers stormed major Blue Zone cities, while Stormriders terrorised the populace from the skies. Huge alien Corrupters roamed the streets, mutating screaming civilians.
Kane, meanwhile, went underground, although he continued to issue orders to his most trusted associates, including LEGION and Alexa Kovacs, while plotting his next move. Meanwhile in Australia, Kilian Qatar assumed leadership of the Brotherhood.
In Europe, the Scrin destroyed many major cities in GDI territory - London and Berne being just two of the most publicised, horrifying cases. At the same time, New Eden in Germany, the crowning achievement of GDI's Tiberium eradication plan, and a vital research hub, fell to the invaders. Though Munich was destroyed, the GDI Commander managed to guide the researchers to safety. Here GDI discovered that Sonic emitters, designed for the destruction of Tiberium, had a powerful effect on the Scrin, damaging them severely. Exploiting this weakness, GDI set to work retaking the destroyed region with a GDI commando, Fullerton rallying his outnumbered troops to victory at Stuttgart. Later GDI successes followed at Cologne and Berne.
Scrin forces also operated elsewhere in Europe, most notably in Croatia, where they come into conflict with both GDI and Nod forces.
Although Kane saw the Scrin as "visitors", not "invaders", LEGION was nevertheless forced to deal with the Traveler-59 subfaction which arrived and started to mind control the Nod-friendly population in the African Red Zone. When LEGION started to destroy their Drone Ships the Scrin brought in an Eradicator Hexapod as reinforcement. LEGION countered it by deploying Nod's own Redeemer.
In China, GDI and Nod troops fighting over the Tacitus were ambushed by a division of the Scrin's dreaded Reaper-17 subfaction. Meteors laden with Tiberium rained down on the city followed by ground troops.
With Kane apparently dead, Kilian Qatar became the de facto leader of Nod although she was suspected of instigating the rebellion at Temple Prime. She recalled all Nod personnel to fight in the last stand in Australia, vowing to retake the world one continent at a time. While a Nod team sent by Qatar was busy hijacking GDI nuclear weapons in transit from the Outback to the main base in Sydney, they were ambushed by the Scrin invasion force which attacked GDI and Nod indiscriminately. Nevertheless, the nuclear weapons were secured.
Kilian Qatar saw that the most logical option was to ally with GDI against this new terrifying enemy, and aided them in the defence of Sydney (while taking the opportunity to steal the nuclear launch codes from GDI). Despite the GDI-Nod Alliance, the Scrin broke through the city's defences and a hasty evacuation of Sydney was ordered. While GDI struggled to hold their ground, the Nod forces received an order from the recently-resurfaced Kane to destroy the GDI forces. The GDI defenders were obliterated with a nuclear missile. Afterwards, Kane reasserted his leadership of Nod at the Battle of Ayers Rock.
With the alien assaults repulsed, both GDI and Nod are now ready to venture into the Red Zones. The ensuing Italian Campaign culminated in the Battle for Kane's Tower and the Battle for Ground Zero, with Kane capturing the only completed Threshold and GDI destroying the Control Node, depriving the aliens of their Tiberium infusement, killing them.