When you realign something, you return it to a former position or place. If you break your arm roller skating, a doctor will have to set the bone, or realign it, before she puts on a cast.
We realign things physically when we line them back up or restore them to a previous balance. The alignment on your car is what makes it drive straight — all four wheels should be perfectly lined up. If they're not, a mechanic can realign them. We can also realign things figuratively, like when a political party realigns itself, or attempts to line its positions up with what's important to voters.