Magellan is planning...
To destroy all the ships thus destroying Luffy's only means of escape. (Thanks to Captn for this idea)
Send the ships away also effectively taking away Luffy's escape.
Enacting 'Suicide No Jutsu' by having all the ships ram into Impel Down only to be revived later by a skinny emo in a wheelchair! XD
Morphing all the ships together to form the Titanic, thus it's destined to sink by a glacier before reaching it's destination point.
I'll tell you in the comments....but I did enjoy your 'Naruto' reference.
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