He wants to kill Rollo for what he did because Rollo tends to think that anything he thinks is harmful for him or his brother must be erased.He couldn't activate the bomb because of Cornelia's action she blew Rollo off.Killing him when he just crashed would arise even more suspicions.
The soldiers in Zero squad are having doubts though they do not understand why it must be done.It seems that V.V has been severely injured maybe the ultimate enemy isn't the Emperor it's just V.V's messing with Lelouch's brain.
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