What?

Masquerading within a survival horror series featuring a former Special Tactics And Rescue Service member.

Resident Evil 5..?

(Blue Stinger is essentially an RE-knockoff with wonky controls)

Correct-o Lady Chalkington.

Proceed!

Ah, thanks.

In this game, it is your goal to gather up pesky things invading your planet and ship them back to where they came from. They like to hide in bushes and on high platforms.

Ape Escape?

Incorrect.

This game also incorporated a little Simon Says minigame within, where you dance to a specific rhythm (or rather replicate the beat.)

Space Channel 5?

Nope.

Hint: You'd gather up these pesky beings in glass jars.

Was the game for the Jaguar? I think I might have heard about this game in an AVGN video.

I think I know what it is... if the game you're thinking of includes mad penguins... Otherwise it's not what I think the game is.

Attack of the Mutant Penguins

No.

Hint: Had a Co-Op mode with the other main character.

For which console is it?

Sega Genesis/Mega Drive. (Also on Wii's virtual console)
All hints so far:
-On Sega Genesis (and Wii virtual console)
-Clearing pests off your planet
-It's a platformer
-Has a copy-the-beat minigame
-Has a co-op mode
-You use glass jars to capture said pests

With which letter/number does the title start?

Oh, come on. Those are ample clues...

Here's a teeny (actually big) hint: the music in the game is very funky.

Toe Jam & Earl?

Toejam & Earl: Panic on Funkotron (the first is an overhead adventure, the second is a sidescroller platformer)

I'll accept that answer, though. Your turn!

Poop.

Me and Rockchalk are winners! Dead Space wedding instead?

Anyway, this game was about a man with extreme multiple personality disorder. So extreme it manifested itself in the form of different physical entities.

(Ok, this just looks like I'm pandering to Rock.)

Haha. Dead Space-Resident Evil-Mortal Kombat wedding for sure!

Anyways, is it killer7?

Bah, Toejam and Earl would have been my second guess... I had a feeling it was anyways, but for some reason the penguins popped in...



I'm going to guess with Indigo Prophecy/Fahrenheit

Edit

The only game like that is indeed "killer 7"
So, if it's ok with Rocky, i'd like to propose a challenge...

If you're certain that's correct (which I think it is), go right ahead.