Chipotle is planning to test a braised, shredded tofu filling as a protein option next month out in San Francisco according to this AP story. They're calling it "Sofritas" and it's cooked similar to the chains' barbacoa.
The tofu will be braised with tomatoes, chipotle sauce, and poblano peppers. Compare that to the barbacoa which is beef braised with chipotle pepper adobo sauce, cumin, cloves, garlic, and oregano.
If the test goes well, expect it to expand to other markets. If successfully added to the menu, tofu would be Chipotles second vegetarian option after their "Vegetarian" option which features vegetarian black beans and guacamole for protein.