Complex sentence: Although he tries to leaves Ace behind, she comes along anyway, leaving a note for the Doctor, suggesting that if she doesn't make it back, he should take Benny as his new companion.
Split into simpler sentences: Although he tries to leave Ace behind, she comes along anyway. Ace, though, leaves a note for the Doctor suggesting that, if she doesn't make it back, he should take Benny as his new companion.