How does the Fama and French 3-factor model explain stock covariance?
It is not clear to what covariance this question refers to. 

As in the CAPM model the covariance among assets is reduced to $\beta$, through the covariance with the market index.

$\beta_i=\sigma_{i,M}/\sigma_M^2$

Then, if CAPM is correct, we could explain the covariance relating the $\beta$s

$\sigma_{i,j}=\beta_i*\beta_j*\sigma_M^2$

In the context of multifactor models something similar occurs, since, in order to use those models, it is necessary to estimate $\beta$s, or sensitivities, related to each proposed factors.