Dalek Sec himself commanded his forces from the skies, whilst the other three members of the Cult fought on the ground. Meanwhile, conflict between the Humans and the Cybermen cost the life of the Cyberleader, however another was quickly created to replace him. As the fighting got out of hand, the Cybermen and the Humans were pushed back by the Daleks and thousands of civilians were shot down in the streets by Daleks.
The Cybermen alone could not defeat the Daleks, but they allied themselves with the Humans and the alliance began to make some progress. Dalek forces were prevented from entering high-priority areas like military bases and large cities. The Cyber-weapons were adapted by the Doctor to be able to pierce Dalek shields, and the advanced weapons of the parrallel human soldiers allowed the Humans to help destroy Daleks too. Thousands of Daleks were shot out of the sky by advanced anti-air railguns mounted on battleships.
But there were millions more Daleks waiting to fight. Slowly the Humans and the Cybermen began to lose significatly. In the end the conflict got so out of control that the Doctor, the last remaining Time Lord, sought the help of Giratina who opened a portal and sucked all the Daleks and Cybermen into the void between worlds.
AftermathDespite the slaughter of the Daleks and Cybermen that ensued, there were some surviviors. The Cult of Skaro managed to escape to New York in the 1930s via an Emergency Temporal Shift, where they began some experiments on pigs that went way out of control.
A small pocket of Cyberman resistance remained after the war, which was explained by either being Cybermen who were somehow trapped during the massacre and thus were not scooped into the Void and therefore survived, or Cybermen that were created during the battle using materials from our universe and were therefore unaffected by the Void. These, coupled with several Cybermen who were later able to escape the Void and fall back in time, later became the Cyberman Remnant.
Following the war, the Daleks went through several ideological changes, particularly after the Final Experiment and Dalek Sec's hybridisation. The Second Galactic War caused the Daleks to doubt their own superiority, causing them to eventually repent and join with the Cybermen in a Dalek-Cyberman Alliance, and even establish their own Parliament.