Throughout most of the series, April and Irma remain the turtles' best human friends. Splinter was once human, Hamato Yoshi, before becoming mutated.
Throughout the Ninja Turtles adventures the humans are in for a rude awakening when they discover that they aren't the only dominate creatures on the planet. There are also different alien lifeforms inhabiting the planet; the Utroms and Triceratons just to name a few. Also, there is the EPF preparing for an alien invasion; led by Agent Bishop and his ruthless army of black-ops commandos. They will exterminate any threat that poses to earth; however sometimes his methods of protection involve the harming of innocent lives. Such as in Bishop's gambit where he took the protection too far and he poses a threat to Earth itself. His army of Bishop clones pose a threat to humans as they will replace the current generation. Thankfully the turtles have destroyed Bishops lab and stopped the madness. The ironic thing is that Earth is constantly invaded by aliens yet the E.P.F that was supposed to be ready was caught off guard. That kind of defeats the purpose of the organizations goal; luckily the turtles are always there to defend Earth from any sort of menace intergalactic or not.
Kraang Prime claims in The Invasion, Part 2 that the Kraang discovered Earth in the distant prehistoric past and sped up evolution by using mutagen on monkeys, who later evolved into humans. Humans can be mutated further by additional exposure to Mutagen.