Raphael saved her from the Foot Clan ninjas and introduced her to the rest of his family. By the end of their first battle with the Shredder, April was part of the family. She even allowed them to move into her new apartment for three weeks until they found a new Lair. Occasionally exasperated by the Turtles' behavior, she has come to rely on them for a good new story and a timely rescue.
Kids grow up and three years later, Allie moved out to go to college. April soon had a new vigilante to report about, the Ronin. The Shredder increased his attacks in response to the Ronin. Casey Jones was hurt in one, and moved into the Lair to recover. April found that she still had strong feelings for him, but what kind of future could you have with a man who tried to get himself killed every night (read Teenage Mutant Ninja Turtles: The Ronin).
Three months after Allie and Mona left New York, Raphael and Zack were drugged by a couple of spherical robots. One of Allie's contacts explained to them that they had been tagged by Val Tech, and advised that they should leave town before Val Tech decided to attack their friends. The Turtles teamed up with a Mutates gang that was traveling to Chicago that night. April couldn't get off work on that short of notice, and someone had to watch Splinter (read Wars Are Won By Those Who Dare: Family, Friends, and Foes).
He bonded with the Turtles and found a sparring partner in the redheaded reporter. He and April have dated off and on in the years since. The Turtles know they can count on him, and have enlisted his help with protecting Splinter (see Teenage Mutant Ninja Turtles III).
Once his year in a juvenile detention hall was completed, Dan made friends with Keno and reunited with Allie, who had just returned home. It was him that Allie ran to after witnessing her brother Billy's murder. He brought Allie and her younger brother Zack to the Turtles, and worked with them to discover the new Shredder (read Teenage Mutant Ninja Turtles: Bloodlines).
Dan, Allie, and Keno all started college together three years later. Around that time, a new vigilante began fighting the Shredder. He and Keno had suspicions about the Ronin's true identity, but didn't say anything because of the Turtles' attitude about their help (read Teenage Mutant Ninja Turtles: The Ronin).
He is also the de facto medic of the group, and his skills have been much tested with Splinter's illness (read Teenage Mutant Ninja Turtles: The Ronin) and Zack's mutation. He was captured and experimented on by Val Tech during the trip to Chicago to fight them, but Donnie tends to look at that experience favorably since it brought him and Di closer together (read Wars Are Won By Those Who Dare: Family, Friends, and Foes).
After Saki's death, his brother Nagi argued that title rightfully belonged to him. The elders of the Foot Clan disagreed, and declared Yoshi a legal heir once again. In order for Nagi to take control, he must defeat Yoshi's heir in combat to the death. Outraged, Nagi brought his supporters to New York, took over what was left from his brother's organization, and sought out Yoshi's descendents to kill them. The Foot Clan sent Clin-san and Lotus Blossom to protect Yoshi's descendents.
After Billy's death, Allie stepped out of the inheritance line, leaving Zack to be trained and become the leader of the Foot Clan (read Teenage Mutant Ninja Turtles: Bloodlines). Nagi was unable to wait and tried to make Zack fight him a mere three years later, only to end up being killed by Allie. His heir, the one Zack will now have to face, is unknown at this time (read Teenage Mutant Ninja Turtles: The Ronin).
But that love was sorely tested by by his brothers' attitudes. After nearly coming to blows with Raph over Allie, she stepped in. No more fighting with the family. While they thought she was being a good girl and staying out of the way, she actually worked around them aided by Mike. He lost patience with the whole act when he figured out she was the Ronin and hadn't told him a thing about that. He tried to make her realize how much that hurt by breaking up with her, but his feelings betrayed themselves when he hurled himself at the Shredder. Allie think he killed Mike, killed the Shredder (read Teenage Mutant Ninja Turtles: The Ronin).
They reunited after three months of her soul searching, fighting Val Tech. Mike had to keep his girl from falling apart as Zack started mutating. His brothers' attitude finally started to change about Allie, especially after Throttle convinced them that they needed her help (read Wars Are Won By Those Who Dare: Family, Friends, and Foes).
And then Raph ran into his own girl, literally. Mona Lisa is a beautiful humanoid salamander, and she doesn't put up with any crap from him or anyone else--an attitude Raph can appreciate. Unfortunately, their first dates got dragged into fighting the Foot Clan and hunting the Ronin. She left with Allie to keep her from committing suicide or something (read Teenage Mutant Ninja Turtles: The Ronin).
But while she was gone, Raph learned what she is--a Mutate--and that she was hunting down the Ronin for her organization. He was devastated and convinced himself that she never felt anything for him. She finally managed to get it through his thick skull that that wasn't the case (read Wars Are Won By Those Who Dare: Family, Friends, and Foes).
They met again many years later, after the Turtles revealed themselves rescuing April O'Neil. Saki, now calling himself the Shredder, kidnapped Splinter, and had his ninjas give the Turtles a sound whipping. Dan Pennington and Casey Jones rescued Splinter, and reunited with his sons, they defeated the Shredder. They thought Casey Jones killed him with a garbage truck (see Teenage Mutant Ninja Turtles).
But the Shredder wasn't dead. Three weeks later, he took back control of what was left of his Foot Clan and set about to take revenge. To that end he kidnapped Dr. Jordan Perry and had him create Tokka and Rahzar. The Turtles defeated his mutants, and then got out of the way when the mutated Shredder tried to bring down a building on all of them (see Teenage Mutant Ninja Turtles II: The Secret of the Ooze).
He raised the Turtles as his sons, and trained them in ninjutsu. He understood better than they did how the reaction from the outside would would most likely be violence. What better way to avoid that than fading away without a trace? Luckily, the few from the outside world that they have made friends have turned out to be loyal friends, but even they echo his need for caution.
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