Malefor's soul was imprisoned in Convexity, and since only a dragon born on the Year of the Dragon, like Cynder, can open the door to his prison, he needed Cynder to gather the energies from the Guardians to set him free.

Once his spirit was freed from Convexity, Malefor awaited for the Night of Eternal Darkness for the Lunar Alignment to take place in order to be resurrected from the Well of Souls where his physical form was imprisoned. When Spyro became infused with the energies of the Lunar Alignment and became Dark Spyro, Malefor took control of him and destroyed Gaul, setting the Dark Master free in the process.  Cynder knocked Spyro out of Malefor's control and soon when the Well of Souls collasped around them. Afterwards, Malefor's spirit was able to return to its physical body and he is resurrected to plague the world in darkness.

Now that I give it some thought, that kind of story sounds terribly cheesy.
But I still think the gameplay was fun.

Rykan wrote:

I haven't understood very well how the events brought to the release of Malefor from his prison in the Dark Realms. Ingitus in A New Beginning tells us that the crystals charged by the guardians open a portal to the Dark Realms, where the Dark Master is been kept. Cynder opens a portal to convexity, an airlock between the Dragon world and the Dark one. From the ending cinematic, I've understood that the portal HAS been open and the Dark MAster should be free... After, in Eternal Night, The Chronicler talks about the Night of Eternal Darkness, its pinnacle the Mountain of Malefor, that summons evil itself and the followers of Malefor. The night comes, Spyro defeats Goul, is tainted by the dark powers... and he's stuck for 3 years in a time bubble, created to protect his friends from the collapse of the mountain. In Dawn of the Dragon, Malefor is in the Dragon Realms again, wagin war over the lands.
Now how that happened?

I don't understand question

Basicly.

Malefor should of been fre'dd by cynder, yet he was'nt as he was still trapped during the whole Night of eternal Darkness.

I think thats the basic aspect of the question

I haven't understood very well how the events brought to the release of Malefor from his prison in the Dark Realms. Ingitus in A New Beginning tells us that the crystals charged by the guardians open a portal to the Dark Realms, where the Dark Master is been kept. Cynder opens a portal to convexity, an airlock between the Dragon world and the Dark one. From the ending cinematic, I've understood that the portal HAS been open and the Dark MAster should be free... After, in Eternal Night, The Chronicler talks about the Night of Eternal Darkness, its pinnacle the Mountain of Malefor, that summons evil itself and the followers of Malefor. The night comes, Spyro defeats Goul, is tainted by the dark powers... and he's stuck for 3 years in a time bubble, created to protect his friends from the collapse of the mountain. In Dawn of the Dragon, Malefor is in the Dragon Realms again, wagin war over the lands.
Now how that happened?

I don't understand question

Basicly Cynders part triggerd the Night of eternal darkness, and theres no real way to stop a luner eclips unless you have a death star, with in the time zone spyro was set...thats a big no....

Once his spirit was freed from Convexity, Malefor awaited for the Night of Eternal Darkness for the Lunar Alignment to take place in order to be resurrected from the Well of Souls where his physical form was imprisoned. When Spyro became infused with the energies of the Lunar Alignment and became Dark Spyro, Malefor took control of him and destroyed Gaul, setting the Dark Master free in the process.  Cynder knocked Spyro out of Malefor's control and soon when the Well of Souls collasped around them. Afterwards, Malefor's spirit was able to return to its physical body and he is resurrected to plague the world in darkness.