Teenage Mutant Ninja Turtles 2003/WMG

The Utrom Shredder is the one who killed Karai's parents.
Karai's parents were Guardians, and Shredder killed her parents so that they could not interfere, he wasn't aware that Karai was their daughter, but he instinctively knew something about her, so he decided to take advantage of this familiarity to raise her as his Dragon.

Ch'rell was an orphan.
Having fallen through the cracks in the Utrom system and forced to make his way by hook or by crook, he now has a sympathetic eye for people with similar histories, i.e., Karai and Hun.
 * He eventually lose sympathies to them both: Karai, for her refusal to kill the Turtles because there's no honor in it, and Hun, due to his constant failures.

There's significance to the way Splinter wears his robe.
It might be a yukata, but it's hard to tell. He wears it right over left, which is normally used to dress a corpse for burial. This could be his own form of mourning for the murder of Hamato Yoshi. Now that, he may switch it to the standard left over right for a Genius Bonus in future episodes, if any.
 * Even if it's not exactly like a Yukata remember that he made it from whatever he could find in the sewers, so this might be as close as he can get.

The Eldritch Abomination is Cthulhu.
It looks exactly like him in "The Darkness Within".
 * Alternate theory: It's one of the Great Old Ones.

Bishop really hates the President.
Think about it: while he's being chewed out by him, he gritted his teeth. It means that Bishop hates the President, and that's the reason why he uses the aliens to kidnap him and almost got him dissected in "Aliens Among Us". The part where Bishop having saved him is to hide the fact that he really hates him.

Bishop is one of the Wesker children.
If you think about it, he has superhuman strength, speed, and being enhanced. However, after being abducted by aliens, it is assumed that he wants nothing to do with Spencer, his creator, and this is why he changed his last name from Wesker to Bishop.

The Utroms are responsible for Ch'rell's behavior
Lets take a minute: why is Ch'rell so evil? why does he focus his efforts to the Utrom, something tells me that the utroms did something to either let him down or did something to him directly.
 * Alternate theory: Ch'rell's evilness is a recessive gene from their pre-utopian days.