The following walkthrough should provide you with objectives for each episode and optional objectives for each episode along with how many apples you can earn from each episode.
Episode 1: Start
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After Episode 0 (the introduction), you'll be taken into your first investigation. The objective is simple: title a Kira. This episode serves as a bit of a tutorial as Ryuk tells Light about the differing roles between L and Kira. Only one apple is obtainable through this episode, and the way to get it is to clear the objective in three turns. Use Soichiro's opinions to your advantage as you try to convince his colleagues that one of them is a mass-murderer. Starting off, Soichiro will be least suspicious of Light's true Kira status as he is his father.
Episode 2: Sweet Tooth
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Hide the fact that your are L from the Kira by targeting another suspect as L. In doing so, you'll be able to find out who the Kira is. Again, since it's an early episode, there is only one obtainable apple. Obtain it by keeping Matsuda's suspicions about you low. If he accuses you once, you won't get the apple.
Episode 3: Contact
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This time you'll be playing as Raye, and FBI agent sent to interrogate the suspects in the Kira case. Your objective is to title a Kira. Get an apple by having no one suspect you on the first vote. L is a reliable asset in this investigation, as he'll have high trust in you from the start. This will help in directing the suspicions away from you and onto the Kira.
Episode 4: Tracking
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For this investigation you'll play as Naomi, who wants to capture Kira in an attempt to get revenge for the death of her fiance. Your main mission will be to find L. The bonus apple can be obtained by arresting Kira after the first voting session. To get the apple, make sure you don't depend on L and only L for the answer to who the Kira is. Interrogate other suspects as they may have a hint to lend you as well.
Episode 5: Decay
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Episode 5 is the first episode where two apples will be obtainable, thus giving you two extra objectives. This time you'll be playing as the father of Light Yagami, Soichiro Yagami. Find out the identity of L to clear the objective and move the story on. For the first apple, clear the objective with Aizawa and Matsuda having their full 100% confidence in you. For the second apple, you'll have to play through the investigation a second time, this time as Soichiro's son, Light Yagami. His objective is to title a Kira. To get the second apple, identify L the first time.
Episode 6: Love
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For the first play-through, you'll be playing as the second Kira, Misa Amane. Find out who L is to clear the main objective. For the first apple, your goal will be to have 100% confidence with Sayu and Soichiro. This mission shouldn't be too hard - you should be able to get it on your first try. For the second play-through, you'll be able to play as Kiyomi Takada, Light's ex-girlfriend. This time, your goal will be to title a Kira. Let nobody be suspicious about you and get Light and Misa's suspicion level at 100 and you can get the second apple.
Episode 7: Watch
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Here you will switch back to Light for the first investigation. The main objective to clear here is to title a Kira and get them arrested. To get the first apple, get arrested during the first three rounds by getting everyone to suspect you as Kira. Do this by letting your words and actions stand out. Make yourself vulnerable to the accusations. For the second investigation, you'll be in control of L again. Label someone L and the investigation will be clear. To complete the episode by getting the second apple, have the full 100% confidence of Soichiro. Do this by first finding your target and then trying to gain Soichiro's suspicions. Doing the second first can get your backing on the wrong target, which will only make him suspect you.
Episode 8: Infiltration
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The number of suspects here has noticeably gone down, but that doesn't mean it's going to be any easier - there are less people to single out, but the suspects will be much more careful with their decisions. For the first time, you'll be playing as Matsuda, the young and naive detective on the Kira Investigation Team lead by L. All you'll have to do for the apple here is clear the objective with no suspicions aimed toward you. The second time, you'll be playing as Misa. For the second apple, avoid getting two votes from the other investigators. Do this by putting getting Soichiro's and Matsuda's confidence up instead of Light's, as they will have less confidence in you to start out with.
Episode 9: Meeting
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Here, you will first play as the Watari. The first objective is to target Kira. For the apple, have each person from the Yotsuba group have at least 50 trust on you before Kira is arrested. For the second investigation as Misa, the main objective will be to title a L while in the 100 confidence stage. For the second apple, get the Kira arrested while your suspicion level is 0.
Episode 10: End
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As Matsuda, title an L to win. Obtain the first apple by having at least 50 confidence from everyone before naming an L. As Light, name a Kira for a victory and for the second apple arrest Kira on the first try.
Episode 11: Divine Kira
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Clear Episode 11 as L by labeling someone Kira. Obtain the apple by arresting first the helper before Kira. Clear Episode 11 as Neo Light by titling someone L. Obtain the apple by killing L at the first round.
Episode 12: L's Successors
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Episode 12 is the bonus episode that moves into an alternate ending where L wins against Kira. This is the first time you'll use Neo Light. The first objective is to find the identity of L. To obtain the apple, have the target worship you but don't arrest them. As L, clear your first objective by finding the one labeled Kira. To obtain the final apple, simply find the target in time for the first voting session.