I play lead guitar in a rock/metal band, and I play downtuned to D standard, my bandmate and rhythm guitarist, he plays guitar like a bass, plays in C standard, and insists in doing so. His reasoning is that C, being a step lower than D will be bassier and take up more low end. I tried explaining why guitars have to be in tune, or at least play in the same key
(which he just does whatever he wants regardless)
and he tried explaining the c is in the same melodic scale as d and will therefore work, along with the downtuning providing more bass freq.
So how much truth is there in that? Is it just bs or will this work without sounding like an out of tune mess?

well I mean as long as he plays the same notes he would otherwise, tuning wouldn't really matter at all. Like if his bass line was D-D-A-F-D or whatever, it wouldn't matter what tuning he's in as long as he keeps playing those notes.
will someone carry me across ten thousand miles under the silence
Ok. But normally he doesn't do that, he thinks that just because it's in C, it will sound like a bass to work with D
It won't sound like a bass. By downtuning he has gained a total of two extra notes (C and C#) over you. Kudos. The bass will sound like a bass, being way lower and having much thicker strings.

Here's a question for you - you have two guitars, why do you want to play the same thing as the other guy?

You should use this experience to learn more about your instrument. If he's chugging away on his low C string, you have your entire fretboard to complement his sound. Chords, arpeggios, harmonies, octave riffs and more are available to you. I'd simply play a different part than him. Even if he were tuned the same I'd play a different part, because playing the same thing all the time renders one guitar pointless.

After re-reading your question, I think it is "guitar number 1 plays a C note, guitar number 2 plays a D note. will it sound crap?".

The answer is yes. If you guys both HAVE to play that open E string, and refuse to tune the same, it'll sound like crap and you should not be in a band together.
And no, Guitar Hero will not help. Even on expert. Really.
As the guys above said, the tuning doesn't really matter, unless you are playing with the same fingerings but in a different tuning. And that's when being able to transpose helps. If you want to play the same riff, you need to use different fingerings. But yeah, as people said, I don't see a point with 2 guitars playing the same stuff all the time. If your friend wants to play lower parts, let him chug on his lowest string. You could play some higher stuff.

But yeah, your friend clearly doesn't know what he's talking about. One step lower tuning is not going to make you sound like bass. And the notes you play need to work together, no matter what register you are playing in. Playing the same riff in C when you are playing it in D just sounds like crap. But as said, what tuning you are in doesn't really matter, as long as you play the same notes/notes that work together (use your ears). So if your friend is in C and you are in D and wants to play the same riff, he needs to play it 2 frets higher.

But seriously, get a bassist if you want a bassier sound.

Also what is your band like? Is it just 2 guitarists? Do you have a drummer? Getting a bassist is pretty important. If your friend wants to play bass parts, tell him to get a bass guitar.
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Your friend is a moron. Guitar is NOT supposed to take up the bass range. If you want a bassier tone, then turn up the bass guitar. (Assuming you have a bass guitar player. If not, get one asap.)
Your friend has absolutely no idea how frequencies or scales work. Tuning down does not make a guitar bassier, it just gives you 2 more notes. And just because C is in the D minor scale, that doesn't mean the C scale is the same. C is the minor 7th of D, meaning unless you are only playing I II IV and V, playing the same fingerings will make you out of key badly, and that's assuming you're playing in Dminor. If you're playing the harmonic minor scale (an extremely common metal scale), he will sound even worse. Not to mention the constant 7th will create a lot of unwanted dissonance. You have to either:
A. Educate him about how his instrument works
B. Get him a bass
C. Play something different to what he his
or D. Kick him out of the band