Regardless of whether there is any grain of truth, the CTO has lost confidence in you. Not just a little bit. He has asked you to leave. The rest of my advice assumes the CEO (your co-founder) has quite a bit of confidence in the CTO. If that is the case, I'm not quite sure you can come back from having the CTO asking you to leave, nor am I certain you should.
I think it would be advisable to talk to a lawyer to see how you can cleanly and professionally leave on your own terms. Save the emotional stuff for friends and your alone time. You will no doubt need to grieve (this was your baby). But I think it would be better for you to be proactive about leaving and professionally extract yourself from this situation. That said, make sure you know your rights and what your contracts entitled you to in such a situation.
Once extracted, take your hurt pride and prove them wrong.