Here are the stories in order ...
Part One
The New Adventures
Operation: Arendelle(Special)
Operation: Dalek part one
Operation: Dalek part two
Prehistoric Invasion(Special)
The Return of the Red Squirrel
Frozen ½ the revenge of the southern isles
The Battle of Madagascar(special)
Earth's Darkest Day part one: The Secrets of Africa
Earth's Darkest Day part two: Collison Course
Conclusion
Elsa and the Riders of Berk (prelude to The DreamWorks War)
The DreamWorks War
Part Two
A Very Penguin October part one
Terror of the Daleks(Special)
The Return of The Destroyer of Worlds
Revenge of The Nanites
Jiggles Returns
Revenge of the Graveyard Eight
Ghost in the Tardis
The Second Dreamworks War
The Battles of Berk
The Siege of Far Far Away
Monsters Vs Daleks
Danger at the bottom of the World
Battle in Metro City
The Final Battle
A Very Penguin October part two
The Nightmare (revenge of Pitch Black)
The Battle before Halloween
Operation: Sub Zero(Special)
Operation: Cold Turkey (special)
Villainmageddon
Part One: Blowhole and Company
Part Two: Attack of The Daleks
Part Three: The Glorious End
Conclusion
Return of the Puffin: Part One
Return of the Puffin: Part Two
Bonus
Penguins of Madagascar: alternate version
Madagascar 3: alternate version
Part Three
A Very Penguin December
Gift of the Daleks
Cyber-men in the Snow
City of the Penguins
Revenge of the polar bears
Day of the emperor penguin
The Second Treasure of the golden Squirrel
Rise of the Phoneix
Return of Dr. Blowhole
Daleks in Russia
return of the octopus
The Frozen Earth
Twelve Days of Daleks
D-day
Wrath of the Daleks
Battle in Seattle
Battle on the moon
Fall of Skaro
The Fall of Dalek-Sec
Battle for Chicago
Dalek offensive (one shot)
War across time and space part one
The Oncoming storm(War across time and space part two)
Return of the Timelords(War across time and space part three)
Christmas Special: The Time of The Daleks
Conclusion
Penguin New Year (one shot)
Part Four
The Newer Adventures(to be updated)
War of the Daleks part one: The planet of war(Special)
War of the Daleks part two: Operation Free Earth (Special)
The Ultimate Adventure
The Cyber-invasion
Tales of Arendelle
The Pirates of Arendelle
Frozen: The musical
The Dalek Invasion of Arendelle
The Surprise (one shot)
Part Five
Penguin Days of Summer part one
Kingdom Come Again
Wrath of Egypt
Yet Another Revenge of Dr. Blowhole
Here comes the Daleks
Revenge of Nanite-Daleks
The Return of the Amarillo Kid(one-shot)
Across the multiverse
Another Earth
Afro Circus Penguins
The Return to the Prime Universe
Into the Medusa Cascade(special)
Penguin Days of Summer part two
Back to The Base
Lost in Prehistoric Times
Night of the Reptiles
The Red Squirrel Strikes Back
Conclusion
Compromised!
Part Six
The Third Dreamworks War
The Return of Drago
Monsters Vs Daleks rematch
Revenge of The Fossa
Battle of the Jade palace
The Battle of New York
The Wrath of Dr. Blowhole
The Fall
Victory of the Puffin
The Three Betrayals
The defeat
The Return(coming soon)
Kowalski: Escape from Seaville(One-shot)
Private: Escape from Hoboken Zoo(one-shot)
Rico: The great Xscape(one-shot)
Skipper: Denmark(One-shot)
Operation: fighting back
Conclusion
Prelude: The Night of the Penguins
The Day of The Penguins(Special)
Extra: Holiday oneshots
Halloween 2015
Christmas 2015
countdown to 2016
Part Seven(WWIII)
The Final DreamWorks War
The Beginning
Monsters vs. Daleks 3
Battle of Europe
Back to the valley of peace
the last battle
Kai's revenge
WWIII
Defcon Five(one shot)
Defcon Red(one shot)
Escalation
World War Dalek
Part one: Judgement of the Daleks
Part Two: Fury of the Daleks
End of the War
Part one: Daleks no more
Part two: Victory!
Conclusion
Wars end(one-shot)