Here are the stories in order ...

Part One(Back in Action)

The New Adventures

Operation: Arendelle(Special)

Operation: Dalek part one

Operation: Dalek part two

Prehistoric Invasion(Special)

The Return of the Red Squirrel

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(Return of The Puffin)

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

Part Three(The Most Dangerous Time of the Year)

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 Dalek

Conclusion

Penguin New Year (one shot)

Part Four(The Ultimate Adventures)

The Newer Adventures

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

Bonus stuff

Kowalski's inventions

Tales of Arendelle

The Pirates of Arendelle

Frozen: The musical

The Dalek Invasion of Arendelle

The Surprise (one shot)

Part Five(Summer of Adventure)

Penguin Days of Summer part one

Kingdom Come Again

Wrath of Egypt

Yet Another Revenge of Dr. Blowhole

Here comes the Daleks

Revenge of the 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 Rise, the Fall, and the Return)

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

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 one shots

Halloween 2015

Christmas 2015

countdown to 2016

Part Seven(WWIII)

The Final DreamWorks War

The Beginning

Monsters vs. Daleks III

Battle of Europe

Back to the valley of peace

the last battle

Kai's revenge

Aftermath(one shot)

WWIII

Defcon One(one shot)

Defcon Red(one shot)

Escalation

World War Dalek

Part one: Judgment of the Daleks

Part Two: Fury of the Daleks

Part Three: Daleks no more(probably)

Part Eight(Summer of Adventure 2016)

More Penguin Days of Summer

So you think you're the elitist of the elite

escape from Komodo

From denmark with revenge

Attack of Professor Blowhole

Endangerous species 2(special)

The day of the peacocks

Wrath of the peacock(three part special)

The Return of the Peacock

The Fury of Lord Shen

The Demise of Lord Shen

More Penguin Days of summer part two

Revenge of the phoenix

Battle of July 4th

The revenge of Mr. Chew

The return of the fishcakes

Caught in the act

Agent Declassified

Conclusion

THE RETURN OF THE SKORCA

Part Nine(across the multiverse II)

Kowalski's Guide to the Multiverse

Part one

Team penguin under attack

Welcome to Jurassic Park?

Where no penguin has gone before

The New Dreamworks War

The Dream Destroyer rises

Showdown in Madagascar

Battle of Gongmon City

Fires of Shanghai

Attack on North Wind

The Final Showdown

Part two

Dr. Bottlenose Vs. Dr. Blowhole(one-shot)

Penguin War

Penguins assemble!

Will the real team penguin please stand up?

Conclusion

Battle of the Multiverse

Part Ten(the holidays)

Halloween terror

Thanksgiving of Doom

A very Penguin Christmas

Gift of the cybermen

Dalek Invasion of Macy's

There is no such thing as Julianary!

Operation: Snowday

The Battle of Christmas Eve(Canceled)

Conclusion

Countdown: 2017(Canceled)

Part Eleven(Unexpected Files)

Ghosts of Zootopia

The ruins of Zootopia

Doom of Zootopia

Battle for Zootopia

The Unexpected Files

Revenge of the cyber-daleks

Jurassic Zoo

The Return of the Wrath of Egypt

Waters of Loch Ness

The Unexpected Files: Into the Hidden World (one shot)

The Warriors of the Golden Squirrel

We meet again Mr. Tux

Conclusion

Nightmares of Madagascar(The Penguins of Madagascar/All Hail King Julian crossover special)

Part Twelve (Epic Adventures)

The Penguins of Madagascar: Awesome Adventures

From Madagascar with Fossa

The Horrible Revenge of Dr. Blowhole(Special)

Into the Penguin

Julien Vs. Julien

Fanfiction

The Officer X files

The Dolphin who loved me(special)

Epic Adventures

The Revenge of Karl

The Future of the Revenge of Dr. blowhole (Special)

An Invention too far(Age of Pentron Part One)

Robot War(Age of Pentron Part Two)

Operation: Jiggli Rescue

Code Red

elitist of the elite 2

The gift of Revenge

Happy New Year?

Dreamwork's

Hiding the Mind Stone(one-shot)

Battle for Power and Dream(one-shot)

The Meeting(one-shot)

Prelude (one-shot)

Infinity War

Conclusion

Endgame

Alternate version series

Penguins of Madagascar: alternate version

Madagascar 3 alternate version

Madly Madagascar Alternate version

Madagascar Escape to Africa Alternate Version

The Penguins Of Madagascar Specials: alternate version