Here’s my 2k3 animated timeline, which is in kind of a weird format.. I haven’t read the Dreamwave comics in years, but I think they split into their own continuity after #3 or #4.
The Turtles and Renet stop Savanti Romero's plan of having the Earth dodge the asteroid that wiped out the dinosaurs.
An evil being called The Shredder rises and terroizes Japan. Emperor Ōjin sends an elite group of warriors known as The Five Dragons to destroy it. Their greatest warrior, Oroku Saki, is secretly seduced into merging with the Tengu just before delivering the killing blow.
After a reign of terror, The Shredder is defeated by the remaining members of The Five Dragons and is imprisoned for what is meant to be eternity.
A faction of Utroms crashland on Earth and set up base in Japan. Their dangerous prisoner Ch'rell escapes.
Ch'rell takes up the identity of The Shredder, re-establishes the Foot Clan and has the Sword of Tengu forged. Since they are being hunted, The Utroms recruit honorable warriors to serve as Guardians and protect them.
Ch'rell eventually uses a magical amulet known as The Heart of Tengu to enslave The Demon Shredder's elemental heralds and uses them as his own mystic warriors.
The Turtles and Renet appear in medieval times while trying to flee Lord Simultaneous, and end up battling Savanti Romero for the first time. Savanti is banished to live among the dinosaurs millions of years in the past.
The Shredder brings the Tokugawa Shogunate to power in Japan, starting the Edo period.
American soldier John Bishop is abducted by aliens during The Battle of New Orleans. Although he undergoes many painful tests, his body is gifted with extremely advanced longevity.
President Ulysses S. Grant establishes the Earth Protection Force. Agent Bishop is placed in charge.
Agent Bishop accquires an alien space ship and a test subject in Roswell, New Mexico.
Hamato Yoshi is born.
A young Yoshi is adopted by The Ancient One.
Tang Shen takes in Splinter as a pet.
Yukio Mashimi betrays Yoshi and the Utroms by murdering Tang Shen and revealing the Utrom's base. They are forced to flee to NYC after being attacked by The Foot.
Yoshi seeks the Ninja Tribunal's aide in battling Shredder. They refuse, since he is merely an imposter of the original.
Shredder most likely adopts Karai around this time.
TCRI is founded in New York.
Casey Jones is born.
April O'Neil is born.
Hamato Yoshi wins the Battle Nexus tournament.
Casey's father is killed by Hun and the Purple Dragons.
Shredder tracks down and kills Yoshi.
Splinter and the Turtles are doused in mutagen after an accident
involving a TCRI truck.
Splinter takes the Turtles to Japan to visit The Ancient One and spread Master Yoshi's ashes.
Serling accidentally appears through a time portal and is claimed by the Turtles as their new toy since he's been reduced to mere inches. He eventually returns to 2007.
Splinter begins training the Turtles in the art of ninjutsu.
The Turtles meet a boy named Arnie (actually Casey Jones) and proceed to train him so he can deal with neighborhood bullies. Michelangelo inadvertently leads him to coin his battlecry: "Goongala!"
Splinter teaches Leonardo to overcome his fear of heights. Leonardo and Raphael fight a giant albino crocodile in the sewers.
The Foot kidnap civilians and genetically alter them to search for the Utroms, who are suspected to be hiding underground.
Splinter wins The Battle Nexus tournament. He is later ambushed by the runner-up Drako, but is saved by Miyamoto Usagi and the Daimyo.
The Turtles turn 15.
The Turtles are forced from their home by Baxter Stockman's Mouser robots and their feud with the Foot clan begins. They meet April O'Neil and Casey Jones.
The Turtles confront The Shredder for the first time. He is defeated by Splinter, but survives.
Shredder attacks the Turtles full-force, destroying April's home in the process. They flee NY with April and Casey, all believed dead by the Foot Clan.
The Turtles return to New York after spending the Winter hiding in Massachusets. Leonardo decapitates The Shredder with the Sword of Tengu and Donatello disables most of the remaining equipment in the Foot Clan's tower. Master Splinter goes missing after being injured in the battle.
The Turtles inflitrate the TCRI building looking for Splinter. They are accidentally transported across the galaxy and meet the Fugitoid, who is on the run from both The Fedaration and Triceraton Republic.
The Turtles and the Fugitoid return to Earth. The Teleportal's activity alerts the Shredder to the location of the Utrom's base and he attacks almost immediately. The Utroms flee to their homeworld in the Theta Galaxy and the Shredder is left in the imploding building. He is assumed dead.
The Turtles turn 16.
With The Shredder gone, the city's gangs are at war. Karai, daughter of The Shredder and head of the Foot Clan in Japan, allies herself with the Turtles to put an end to the chaos. A truce is made between the Foot and the Turtles.
The Shredder once again emerges from his apparent death and breaks the truce, putting Karai at conflict between her honor and her duty.
Michelangelo wins the Battle Nexus tournament.
A Christmas feast is held at the lair. Michelangelo adopts Klunk.
The Triceratons invade Earth in seach of the Fugitoid. The Turtles encounter Agent Bishop for the first time. The Fugitoid cripples both the Triceraton Republic and The Federation by uploading a virus into their systems. Traximus overthrows the current Triceraton regime and brings peace between them and the Federation.
The Turtles turn 17.
The Shredder launches his star-ship made from salvaged Triceraton technology, and the Turtles and Splinter nearly die trying to stop him, but they are saved at the last second by the Utroms. He is found guilty by an Utrom jury and is sentenced to be exiled for life on an icy asteroid. Karai vows vengeance.
The Turtles and Splinter recover in Northhampton after the battle. They come back to New York fully healed, but Leonardo can not forgive himself for his failure. Splinter sends him to seek the Ancient One after realizing that there is nothing more he can do for his troubled son.
Karai assumes the mantle of The Shredder. She attacks and destroys the Turtle's home while Leonardo is still training in Japan.
The Turtles battle a mutant outbreak accidentally caused by Agent Bishop. Donatello is unknowingly infected and mutates further some time later.
The Turtles rescue a mutated Donatello by retreiving the Heart of Tengu for Bishop, who is tricked into destroying it, thus releasing The Shredder's Heralds (the Foot Mystics). They immediately begin their quest to resurrect their master, the original Shredder.
The Turtles are summoned to Japan to train under the Ninja Tribunal.
The Turtles turn 18.
The Turtles battle the ressurected Tengu Shredder alongside all the allies they can gather. The spirit of Hamato Yoshi destroys him for good. Karai lets go of her vendetta against the Turtles.
The Turtles are sucked into the future by Cody Jones.
The Turtles turn 19 and become Chunin while trapped in the future.
After 1 year, the Turtles return from the future and spend months battling the new Cyber Shredder and recovering Splinter's lost data bits.
April and Casey get married in Northampton. Serling is sent back to the future some time after the wedding.
The Turtles and Splinter return to The Battle Nexus for another tournament. The results are unknown.
The Turtles team up with their Fred Wolf cartoon and Mirage comic book counterparts to stop The Shredder once and for all before he destroys the multi-verse.
The Turtles turn 20.
Bishop and Stockman's alien lab is destroyed by accident but Bishop is rescued by one of his alien prisoners.
Cody Jones is born.
The Turtles and Splinter appear in the future and meet April and Casey's great-grandson Cody Jones. They battle many new enemies, and discover that Bishop is now a world leader.
The Turtles kill Sh'oKanabo and seemingly delete Viral, ending any threat of the Day of Awakening for good.
The Turtles and Cody go on several unseen adventures. They meet Space Usagi, battle a Triceraton Shredder, and possibly aide the Dark Turtles in turning against Darius Dunn. They celebrate their 19th birthday around this time.
Cody sends the Turtles back to their time. There is a malfunction caused by Viral, and Serling is accidentally sent back too. Luckily, Cody gets the time machine working again some time later.