My Favorite episodes of Star Trek Voyager

The Voyager crew has entered Borg Space, luckily they find a thin passage fillied with Gravametric distortions but devoid of Borg activity. They Dub it  "The Northwest Passage" On the way there they find a graveyard of fifteen destroyed Borg Cubes. They have encountered Species 8472, a very powerful and extremely Xenophobic race of aliens who are at war with the Borg. 

Janeway decides to make a deal with the devil; Team up with the Borg to take down a common foe. The Collective agrees and dispatches Seven of Nine, Tertiary Adjunct of Unimatrix Zero-One, to work with the voyager crew.

One of my top favorite episodes.

Voyager has come across a unknown part of space. They are hailed by a small vessel, the commander of the vessel claims that they are trespassing in Krenim territory. Janeway Orders that the course be maintained. Later on they are befriended by the Zhal who claim the Krenim are nothing but a mere annoyance and that they were defeated long ago. Suddenly a massive Spatial Distortion appears, The Zhal ships disappear and The Small Krenim ship becomes a Massive Warship.

So begins the Year of Hell. For one year the Voyager crew do battle against The Krenim Imperium, and their deadly temporal weapons capable of erasing events and people from time.

After upgrading the sensors the crew find an abandoned alien sensor network. Through the network they locate a Federation vessel on the edge of the Alpha Quadrant. They try to send a signal but it degrades on the way. So they decide to send the Doctor instead, compressed in a datastream. He finds himself in the sickbay of the USS Prometheus, an experimental Starfleet vessel taken over by Romulans. (this was before they joined The Federation Alliance)

Voyager finds itself trapped in a Subspace Corridor, while looking for a way out they are approached by a Turei vessel. They help Voyager out of the corridor but demand to board the ship and delete all records of it. Janeway refuses and the Turei open fire. Voyager finds refuge on an Unknown planet suffering a nuclear winter. Faint life signs are detected under a destroyed city, its the Vaadwaur ancient enemy of the Turei.
 

The crew has a near miss with a Graviton Ellipse, because these phenomena are very rare a probe is launched to explore in inside.  They are amazed by what they find inside 28 billion compound, and the crown jewel, The Ares IV Command module. One of earths early manned missions to Mars,  notorious for the disappearance of the module and its commander John Kelly in 2037.

The crew is on A much needed shore leave, instead of  taking some R&R on the planet below Seven and Tuvok decide to take a shuttle to Study a near by micro nebula. On the way there they are attacked and kidnapped by Penk, Tuvok is seriously injured and Seven is forced to take part in the brutal Tsunkatse matches.

Now that they are in range of the Alpha Quadrant Voyager is now able to communicate with Starfleet on a Daily Basis. During this time the Doctor sends a rough Draft of his Holonovel to be published, unfortunately The Doctor uses his situation as a basis for the story and portrays the crew in a bad light. After deciding to make some changes to the Novel he finds out its been released with out his permission. This sparks a debate on Photonic Rights.